diff options
| author | Shepherd on Tux02 | 2024-06-20 08:37:15 -0500 |
|---|---|---|
| committer | Shepherd on Tux02 | 2024-06-20 08:37:15 -0500 |
| commit | fe5fd5cb23907f8e37edafda96bafa608a3e0e7f (patch) | |
| tree | 0b4cec2038dde07fe26f1c6882369f36a9545a19 | |
| parent | f0f8dc84eca7088177797f84db05314537615c77 (diff) | |
| parent | 0362ee068a39ce9a5fd6f0fba9cd5586211f07f1 (diff) | |
| download | guix-bioinformatics-fe5fd5cb23907f8e37edafda96bafa608a3e0e7f.tar.gz | |
Merge branch 'master' of /home/git/public/guix-bioinformatics
| -rw-r--r-- | .guix-channel | 2 | ||||
| -rw-r--r-- | gn/packages/bioinformatics.scm | 1576 | ||||
| -rw-r--r-- | gn/packages/crates-io.scm | 203 | ||||
| -rw-r--r-- | gn/packages/cwl.scm | 84 | ||||
| -rw-r--r-- | gn/packages/datastructures.scm | 117 | ||||
| -rw-r--r-- | gn/packages/file-systems.scm | 27 | ||||
| -rw-r--r-- | gn/packages/genenetwork.scm | 664 | ||||
| -rw-r--r-- | gn/packages/globus.scm | 76 | ||||
| -rw-r--r-- | gn/packages/java.scm | 96 | ||||
| -rw-r--r-- | gn/packages/javascript.scm | 347 | ||||
| -rw-r--r-- | gn/packages/julia.scm | 1293 | ||||
| -rw-r--r-- | gn/packages/maths.scm | 108 | ||||
| -rw-r--r-- | gn/packages/ocaml.scm | 25 | ||||
| -rw-r--r-- | gn/packages/python.scm | 165 | ||||
| -rw-r--r-- | gn/packages/ratspub.scm | 16 | ||||
| -rw-r--r-- | gn/packages/riscv.scm | 1 | ||||
| -rw-r--r-- | gn/packages/ruby.scm | 10 | ||||
| -rw-r--r-- | gn/packages/virtualization.scm | 5 | ||||
| -rw-r--r-- | gn/services/bh20-seq-resource-container.scm | 110 | ||||
| -rw-r--r-- | gn/services/pluto.scm | 17 | ||||
| -rw-r--r-- | lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch | 111 | ||||
| -rw-r--r-- | seqwish-paryfor-riscv.diff | 20 | ||||
| -rw-r--r-- | seqwish-shared-library.diff | 195 |
23 files changed, 4114 insertions, 1154 deletions
diff --git a/.guix-channel b/.guix-channel index e42b9ad..e7e9a9a 100644 --- a/.guix-channel +++ b/.guix-channel @@ -14,7 +14,7 @@ (name guix) (url "https://git.savannah.gnu.org/git/guix.git") (branch "master") - (commit "d4e9ad2d42dddf06a8f1b01c9f49fee16c592d75") + (commit "b0b988c41c9e0e591274495a1b2d6f27fcdae15a") (introduction (channel-introduction (version 0) diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index db420b7..ed6d4d4 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -16,11 +16,14 @@ #:use-module (guix build-system meson) #:use-module (guix build-system ocaml) #:use-module (guix build-system python) + #:use-module (guix build-system r) #:use-module (guix build-system trivial) #:use-module (guix build-system waf) #:use-module (gnu packages) #:use-module (gn packages crates-io) + #:use-module (gn packages datastructures) #:use-module (gn packages java) + #:use-module (gn packages maths) #:use-module (gn packages ocaml) #:use-module (gn packages python) #:use-module (gnu packages algebra) @@ -39,6 +42,7 @@ #:use-module (gnu packages cpp) #:use-module (gnu packages cran) #:use-module (gnu packages crates-io) + #:use-module (gnu packages crates-graphics) #:use-module (gnu packages curl) #:use-module (gnu packages databases) #:use-module (gnu packages datastructures) @@ -47,6 +51,7 @@ #:use-module (gnu packages fontutils) #:use-module (gnu packages gcc) #:use-module (gnu packages ghostscript) + #:use-module (gnu packages graph) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) #:use-module (gnu packages image) @@ -60,6 +65,7 @@ #:use-module (gnu packages mpi) #:use-module (gnu packages ncurses) #:use-module (gnu packages ocaml) + #:use-module (gnu packages parallel) #:use-module (gnu packages perl) #:use-module (gnu packages pkg-config) #:use-module (gnu packages protobuf) @@ -194,6 +200,100 @@ accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave.") (license license:gpl3))) +(define-public wfmash-x86-64-v2 + (package/inherit wfmash + (name "wfmash-x86-64-v2") + (arguments + (substitute-keyword-arguments (package-arguments wfmash) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v2" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v2" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v2")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-binary + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +(define-public wfmash-x86-64-v3 + (package/inherit wfmash + (name "wfmash-x86-64-v3") + (arguments + (substitute-keyword-arguments (package-arguments wfmash) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v3" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v3" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v3")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-binary + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +(define-public wfmash-x86-64-v4 + (package/inherit wfmash + (name "wfmash-x86-64-v4") + (arguments + (substitute-keyword-arguments (package-arguments wfmash) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v4" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v4" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v4")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-binary + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +;; This copy of wfmash will automatically use the libraries that target the +;; x86_64 psABI which the hardware supports. +(define-public wfmash-hwcaps + (package/inherit wfmash + (name "wfmash-hwcaps") + (arguments + (substitute-keyword-arguments (package-arguments wfmash) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'install-optimized-libraries + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((hwcaps "/lib/glibc-hwcaps")) + (copy-recursively + (string-append (assoc-ref inputs "wfmash-x86-64-v2") + hwcaps "/x86-64-v2") + (string-append #$output hwcaps "/x86-64-v2")) + (copy-recursively + (string-append (assoc-ref inputs "wfmash-x86-64-v3") + hwcaps "/x86-64-v3") + (string-append #$output hwcaps "/x86-64-v3")) + (copy-recursively + (string-append (assoc-ref inputs "wfmash-x86-64-v4") + hwcaps "/x86-64-v4") + (string-append #$output hwcaps "/x86-64-v4"))))))))) + (native-inputs + (modify-inputs (package-native-inputs wfmash) + (append wfmash-x86-64-v2 + wfmash-x86-64-v3 + wfmash-x86-64-v4))) + (properties `((tunable? . #f))))) + (define-public freec (package (name "control-freec") @@ -469,7 +569,7 @@ reads.") (define-public gfaffix (package (name "gfaffix") - (version "0.1.3") + (version "0.1.5") (source (origin (method git-fetch) @@ -478,12 +578,7 @@ reads.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1biss5qv6ag1dfkn1nspwd528hpzgn8i4jydvbv2z7yv7sc685rh")) - (modules '((guix build utils))) - (snippet - '(begin - (substitute* "Cargo.toml" - (("^handlegraph.*") "handlegraph = \"0.7\"\n")))))) + (base32 "181jxl8ldj39jgscyqzhz4l4k5kxj1j9hvzi8dxj59h2zzznb0kb")))) (build-system cargo-build-system) (arguments `(#:install-source? #f @@ -491,19 +586,12 @@ reads.") (("rust-clap" ,rust-clap-3) ("rust-rustc-hash" ,rust-rustc-hash-1) ("rust-regex" ,rust-regex-1) - ("rust-handlegraph" ,rust-handlegraph-0.7) + ("rust-handlegraph" ,rust-handlegraph-0.7.0-alpha.9) ("rust-gfa" ,rust-gfa-0.10) ("rust-quick-csv", rust-quick-csv-0.1) + ("rust-rayon" ,rust-rayon-1) ("rust-log" ,rust-log-0.4) - ("rust-env-logger" ,rust-env-logger-0.7)) - #:phases - (modify-phases %standard-phases - (add-after 'unpack 'adjust-dependency-version - (lambda* (#:key inputs #:allow-other-keys) - (let ((handlebar-version ,(package-version rust-handlegraph-0.7))) - (substitute* "Cargo.toml" - (("\"0.7\"") - (string-append "{ version = \"" handlebar-version "\" }"))))))))) + ("rust-env-logger" ,rust-env-logger-0.7)))) (home-page "https://github.com/marschall-lab/GFAffix") (synopsis "Identify walk-preserving shared affixes in variation graphs") (description @@ -511,6 +599,117 @@ reads.") collapses them into a non-redundant graph structure.") (license license:expat))) +(define-public vcfbub + (package + (name "vcfbub") + (version "0.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pangenome/vcfbub") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0sk2ab22z6qa00j1w8a8f5kbb7q2xb10fhd32zy4lh351v3mqmyg")))) + (build-system cargo-build-system) + (arguments + `(#:install-source? #f + #:cargo-inputs + (("rust-clap" ,rust-clap-2) + ("rust-flate2" ,rust-flate2-1) + ("rust-vcf" ,rust-vcf-0.6)))) + (home-page "https://github.com/pangenome/vcfbub") + (synopsis "Popping bubbles in vg deconstruct VCFs") + (description + "The VCF output produced by a command like @command{vg deconstruct -e -a +-H '#' ...} includes information about the nesting of variants. With @code{-a}, +@code{--all-snarls}, we obtain not just the top level bubbles, but all nested +ones. This exposed snarl tree information can be used to filter the VCF to +obtain a set of non-overlapping sites (n.b. \"snarl\" is a generic model of +graph bubbles including tips and loops). +@code{vcfbub} lets us do two common operations on these VCFs: +@enumerate +@item We can filter sites by maximum level in the snarl tree. For instance, +@code{--max-level 0} would keep only sites with @code{LV=0}. In practice, vg's +snarl finder ensures that these are sites rooted on the main linear axis of the +pangenome graph. Those at higher levels occur within larger variants. +@item We can filter sites by maximum allele size, either for the reference +allele or any allele. In this case, @code{--max-ref-length 10000} would keep +only sites where the reference allele is less than 10kb long. Setting +@code{--max-ref-length} or @code{--max-allele-length} additionally ensures that +the output contains the bubbles nested inside of any popped bubble, even if +they are at greater than @code{--max-level}. +@end enumerate +@code{vcfbub} accomplishes a simple task: we keep sites that are the children +of those which we \"pop\" due to their size. These occur around complex large +SVs, such as multi-Mbp inversions and segmental duplications. We often need to +remove these, as they provide little information for many downstream +applications, such as haplotype panels or other imputation references.") + (license license:expat))) + +(define-public fastix + (package + (name "fastix") + (version "0.1.0") + (source (origin + (method url-fetch) + (uri (crate-uri "fastix" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 "1mzk65mg8vx0hz39xis6zqdmq56abhmza656gn9pgmlsn151gpx2")))) + (build-system cargo-build-system) + (arguments + `(#:install-source? #f + #:cargo-inputs + (("rust-clap" ,rust-clap-2)) + #:cargo-development-inputs + (("rust-assert-cmd" ,rust-assert-cmd-0.12) + ("rust-predicates" ,rust-predicates-1)))) + (home-page "https://github.com/ekg/fastix") + (synopsis "Prefix-renaming FASTA records") + (description "A command line tool to add prefixes to FASTA headers. The +idea is to support pangenomic applications, following the +@url{https://github.com/pangenome/PanSN-spec, PanSN} hierarchical naming +specification.") + (license license:expat))) + +(define-public pafplot + (let ((commit "7dda24c0aeba8556b600d53d748ae3103ec85501") + (revision "1")) + (package + (name "pafplot") + (version (git-version "0.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/pafplot.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "04ffz0zfj4mvfxmrwgisv213fypgl02f7sim950a067pm7375g1l")))) + (build-system cargo-build-system) + (arguments + `(#:install-source? #f + #:cargo-inputs + (("rust-clap" ,rust-clap-2) + ("rust-boomphf" ,rust-boomphf-0.5) + ("rust-itertools" ,rust-itertools-0.10) + ("rust-fnv" ,rust-fnv-1) + ("rust-lodepng" ,rust-lodepng-3) + ("rust-rgb" ,rust-rgb-0.8) + ("rust-line-drawing" ,rust-line-drawing-0.8)))) + (home-page "https://github.com/ekg/pafplot.git") + (synopsis "Base-level dotplots from PAF alignments") + (description "In the process of generating alignments between whole +genomes, we often need to understand the base-level alignment between +particular sequences. @command{pafplot} allows us to do so by rasterizing the +matches alignment set. It draws a line on a raster image to represent each +match found in a set of alignments. The resulting image provides a high-level +view of the structure of the alignments, and in consequence the homology +relationships between the sequences in consideration.") + (license license:expat)))) + (define-public gafpack (let ((commit "ad31875b6914d964c6fd72d1bf334f0843538fb6") ; November 10, 2022 (revision "1")) @@ -1399,120 +1598,82 @@ runApp(launch.browser=0, port=4208)~%\n" (scRNA-seq) data analysis.") (license license:agpl3)))) -(define-public seqwish-0.1 +(define-public seqwish (package (name "seqwish") - (version "0.1") + (version "0.7.9") (source (origin (method git-fetch) (uri (git-reference (url "https://github.com/ekg/seqwish.git") - (commit (string-append "v" version)))) + (commit (string-append "v" version)) + (recursive? #t))) (file-name (git-file-name name version)) (sha256 - (base32 - "1gp72cmi13hbkmwwhgckmxkbx8w644jc5l6dvvvxdbl6sk8xsi5r")))) - (build-system gnu-build-system) + (base32 "0xnv40kjlb610bk67n4xdqz5dfsjhrqld5bxzblji57k6bb4n66x")) + (patches (search-patches "seqwish-paryfor-riscv.diff" + "seqwish-shared-library.diff")) + (snippet + #~(begin + (use-modules (guix build utils)) + (substitute* '("CMakeLists.txt" + "deps/atomic_queue/Makefile" + "deps/mmmulti/deps/DYNAMIC/CMakeLists.txt" + "deps/mmmulti/deps/atomic_queue/Makefile" + "deps/mmmulti/deps/ips4o/CMakeLists.txt") + (("-march=native") "") + (("-mcx16") "")) + (substitute* '("deps/mmmulti/deps/sdsl-lite/CMakeLists.txt" + "deps/sdsl-lite/CMakeLists.txt") + (("-msse4.2 -march=native") "")))))) + (build-system cmake-build-system) (arguments - `(#:phases + `(#:configure-flags + (cons* ,@(if (target-x86?) + ;; This is the minimum needed to compile on x86_64, and is a + ;; subset of any other optimizations which might be applied. + '("-DCMAKE_C_FLAGS=-mcx16" + "-DCMAKE_CXX_FLAGS=-mcx16") + '()) + '("-DSEQWISH_LINK_SHARED_LIBRARY=ON")) + #:phases (modify-phases %standard-phases - (delete 'configure) - (replace 'build + (add-after 'unpack 'set-version + (lambda _ + ;; This stashes the build version in the executable. + (mkdir "include") + (substitute* "CMakeLists.txt" + (("^execute_process") "#execute_process")) + (with-output-to-file "include/seqwish_git_version.hpp" + (lambda () + (format #t "#define SEQWISH_GIT_VERSION \"~a\"~%" ,version))))) + (add-after 'unpack 'link-with-some-shared-libraries (lambda* (#:key inputs #:allow-other-keys) - (let ((sdsl-lite (assoc-ref inputs "sdsl-lite")) - (sufsort (assoc-ref inputs "sufsort")) - (bsort (assoc-ref inputs "bsort")) - (mmap_allocator (assoc-ref inputs "mmap-allocator")) - (tayweeargs (assoc-ref inputs "tayweeargs-source")) - (gzipreader (assoc-ref inputs "gzipreader-source")) - (mmmultimap (assoc-ref inputs "mmmultimap-source")) - (iitii (assoc-ref inputs "iitii-source")) - (ips4o (assoc-ref inputs "ips4o-source"))) - (apply invoke "g++" "-o" "seqwish" - "-O3" "-g" "-std=c++14" "-fopenmp" - "-latomic" "-lz" - (string-append "-I" sdsl-lite "/include") - (string-append "-I" sdsl-lite "/include/sdsl") - (string-append "-I" bsort "/include") - (string-append "-I" tayweeargs) - (string-append "-I" gzipreader) - (string-append "-I" mmmultimap "/src") - (string-append "-I" iitii "/src") - (string-append "-I" mmap_allocator "/include") - (string-append "-I" ips4o) - (append - (find-files "src" ".") - (list - (string-append sdsl-lite "/lib/libsdsl.so") - (string-append sufsort "/lib/libdivsufsort.so") - (string-append sufsort "/lib/libdivsufsort64.so") - (string-append mmap_allocator "/lib/libmmap_allocator.a") - (string-append bsort "/lib/libbsort.a"))))))) + (substitute* '("CMakeLists.txt" + "deps/mmmulti/CMakeLists.txt") + (("\".*libsdsl\\.a\"") "\"-lsdsl\"") + (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"") + (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"") + (("\\$\\{sdsl-lite_INCLUDE\\}") + (search-input-directory inputs "/include/sdsl")) + (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}") + (dirname + (search-input-file inputs "/include/divsufsort.h")))))) (replace 'check - (lambda _ + (lambda* (#:key tests? #:allow-other-keys) ;; Add seqwish to the PATH for the tests. (setenv "PATH" (string-append (getcwd) ":" (getenv "PATH"))) - (with-directory-excursion "test" - (invoke "make")))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (install-file "seqwish" (string-append out "/bin"))) - #t))))) + (when tests? + (with-directory-excursion "../source/test" + (invoke "make")))))))) (inputs - `(("bsort" ,ekg-bsort) - ("mmap-allocator" ,ekg-mmap-allocator) - ("openmpi" ,openmpi) - ("sdsl-lite" ,sdsl-lite) - ("sufsort" ,libdivsufsort) - ("zlib" ,zlib))) + (list jemalloc + libdivsufsort + openmpi + sdsl-lite + zlib)) (native-inputs - `(("prove" ,perl) - ("tayweeargs-source" ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/Taywee/args.git") - (commit "3de44ec671db452cc0c4ef86399b108939768abb"))) - (file-name "tayweeargs-source-for-seqwish") - (sha256 - (base32 - "1v8kq1gvl5waysrfp0s58881rx39mnf3ifdsl6pb3y3c4zaki2xh")))) - ("gzipreader-source" ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/gatoravi/gzip_reader.git") - (commit "0ef26c0399e926087f9d6c4a56067a7bf1fc4f5e"))) - (file-name "gzipreader-source-for-seqwish") - (sha256 - (base32 - "1wy84ksx900840c06w0f1mgzvr7zsfsgxq1b0jdjh8qka26z1r17")))) - ("mmmultimap-source" ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/mmmultimap.git") - (commit "88c734c36563048b0f3acc04dd8856f19e02b75f"))) - (file-name "mmmultimap-source-for-seqwish") - (sha256 - (base32 - "06mnf3bd32s3ngxkl573ylg2qsvlw80r1ksdwamx3fzxa1a5yls0")))) - ("iitii-source" ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/iitii.git") - (commit "85209e07a3ee403fb6557387a7f897cd76be4406"))) - (file-name "iitii-source-for-seqwish") - (sha256 - (base32 - "0sszvffkswf89nkbjmjg3wjwqvy2w0d3wgy3ngy33ma4sy4s025s")))) - ("ips4o-source" ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/SaschaWitt/ips4o.git") - (commit "bff3ccf0bf349497f2bb10f825d160b792236367"))) - (file-name "ips4o-source-for-seqwish") - (sha256 - (base32 - "0yjfvrkiwgmy5cn0a7b9j8jwc3zp0l8j4dl5n0jgz68pdnhlp96h")))))) + (list perl)) (home-page "https://github.com/ekg/seqwish") (synopsis "Alignment to variation graph inducer") (description "Seqwish implements a lossless conversion from pairwise @@ -1525,77 +1686,212 @@ large inputs that are commonly encountered when working with large numbers of noisy input sequences. Memory usage during construction and traversal is limited by the use of sorted disk-backed arrays and succinct rank/select dictionaries to record a queryable version of the graph.") + (properties `((tunable? . #t))) (license license:expat))) -(define ekg-bsort - (let ((commit "c3ab0d3308424030e0a000645a26d2c10a59a124") - (revision "1")) - (package - (name "bsort") - (version (git-version "0.0.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/bsort.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "0dgpflzcp3vdhbjwbjw347czi86gyk73hxcwjdqnaqh5vg61bdb6")))) - (build-system cmake-build-system) - (arguments - '(#:tests? #f ; no test target - #:out-of-source? #f - #:phases - (modify-phases %standard-phases - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (install-file "bin/bsort" (string-append out "/bin")) - (install-file "src/bsort.hpp" (string-append out "/include")) - (install-file "lib/libbsort.a" (string-append out "/lib"))) - #t))))) - (home-page "") - (synopsis "") - (description "") - (license license:gpl2)))) +(define-public seqwish-x86-64-v2 + (package/inherit seqwish + (name "seqwish-x86-64-v2") + (outputs '("out" "static")) + (arguments + (substitute-keyword-arguments (package-arguments seqwish) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v2" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v2" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v2")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))) + (add-after 'install 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v2/libseqwish.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t) + (tunable? . #f))))) -(define ekg-mmap-allocator - (let ((commit "ed61daf094de1c2e1adbe8306287ad52da5f0264") - (revision "1")) - (package - (name "mmap-allocator") - (version (git-version "0.10.1" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/mmap_allocator.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 - "1f30b2kpwwzh6333s0qi5samk458ghbnvyycf6rwx6n6j7xswhbw")))) - (build-system gnu-build-system) - (arguments - '(#:phases - (modify-phases %standard-phases - (delete 'configure) ; no configure script - (add-before 'install 'pre-install - (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) +(define-public seqwish-x86-64-v3 + (package/inherit seqwish + (name "seqwish-x86-64-v3") + (outputs '("out" "static")) + (arguments + (substitute-keyword-arguments (package-arguments seqwish) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v3" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v3" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v3")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))) + (add-after 'install 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v3/libseqwish.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t) + (tunable? . #f))))) + +(define-public seqwish-x86-64-v4 + (package/inherit seqwish + (name "seqwish-x86-64-v4") + (outputs '("out" "static")) + (arguments + (substitute-keyword-arguments (package-arguments seqwish) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v4" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v4" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v4")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")))) + (add-after 'install 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v4/libseqwish.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t) + (tunable? . #f))))) + +;; This copy of seqwish will automatically use the libraries that target the +;; x86_64 psABI which the hardware supports. +(define-public seqwish-hwcaps + (package/inherit seqwish + (name "seqwish-hwcaps") + (arguments + (substitute-keyword-arguments (package-arguments seqwish) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'install-optimized-libraries + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((hwcaps "/lib/glibc-hwcaps")) + (copy-recursively + (string-append (assoc-ref inputs "seqwish-x86-64-v2") + hwcaps "/x86-64-v2") + (string-append #$output hwcaps "/x86-64-v2")) + (copy-recursively + (string-append (assoc-ref inputs "seqwish-x86-64-v3") + hwcaps "/x86-64-v3") + (string-append #$output hwcaps "/x86-64-v3")) + (copy-recursively + (string-append (assoc-ref inputs "seqwish-x86-64-v4") + hwcaps "/x86-64-v4") + (string-append #$output hwcaps "/x86-64-v4"))))))))) + (native-inputs + (modify-inputs (package-native-inputs seqwish) + (append seqwish-x86-64-v2 + seqwish-x86-64-v3 + seqwish-x86-64-v4))) + (properties `((tunable? . #f))))) + +(define-public smoothxg + (package + (name "smoothxg") + (version "0.7.2") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/pangenome/smoothxg" + "/releases/download/v" version + "/smoothxg-v" version ".tar.gz")) + (sha256 + (base32 "1px8b5aaa23z85i7ximdamk2jj7wk5hb7bpbrgxsvkxc69zlwy38")) + (snippet + #~(begin + (use-modules (guix build utils)) + (substitute* (find-files "." "CMakeLists.txt") + (("spoa_optimize_for_native ON") + "spoa_optimize_for_native OFF") + (("-msse4\\.2") "") + (("-march=native") "")))))) + (build-system cmake-build-system) + (arguments + (list + #:make-flags + #~(list (string-append "CC = " #$(cc-for-target))) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'link-with-some-shared-libraries + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("CMakeLists.txt" + "deps/mmmulti/CMakeLists.txt" + "deps/odgi/deps/mmmulti/CMakeLists.txt") + (("\".*libsdsl\\.a\"") "\"-lsdsl\"") + (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"") + (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"") + (("\".*libodgi\\.a\"") "\"-lodgi\"") + (("\\$\\{sdsl-lite_INCLUDE\\}") + (search-input-directory inputs "/include/sdsl")) + (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}") + (dirname + (search-input-file inputs "/include/divsufsort.h"))) + (("\\$\\{odgi_INCLUDE\\}") + (search-input-directory inputs "/include/odgi"))))) + (add-before 'build 'build-abPOA + (lambda* (#:key make-flags #:allow-other-keys) + ;; This helps with portability to other architectures. + (with-directory-excursion + (string-append "../smoothxg-v" #$version "/deps/abPOA") (substitute* "Makefile" - (("HEADERS=") "HEADERS=mmappable_vector.h ") - (("/usr") out)) - (mkdir-p (string-append out "/lib")) - (mkdir (string-append out "/include")) - #t)))) - #:test-target "test")) - (home-page "") - (synopsis "") - (description "") - (license license:lgpl2.0+)))) ; README just says "lpgl". + (("-march=native") "")) + (apply invoke "make" "libabpoa" make-flags))))))) + (inputs + (list jemalloc + libdivsufsort + odgi + openmpi + pybind11 + python + sdsl-lite + zlib + (list zstd "lib"))) + (native-inputs + (list pkg-config)) + (home-page "https://github.com/ekg/smoothxg") + (synopsis + "Linearize and simplify variation graphs using blocked partial order alignment") + (description "Pangenome graphs built from raw sets of alignments may have +complex local structures generated by common patterns of genome variation. +These local nonlinearities can introduce difficulty in downstream analyses, +visualization, and interpretation of variation graphs. + +@command{smoothxg} finds blocks of paths that are collinear within a variation +graph. It applies partial order alignment to each block, yielding an acyclic +variation graph. Then, to yield a smoothed graph, it walks the original paths +to lace these subgraphs together. The resulting graph only contains cyclic or +inverting structures larger than the chosen block size, and is otherwise +manifold linear. In addition to providing a linear structure to the graph, +smoothxg can be used to extract the consensus pangenome graph by applying the +heaviest bundle algorithm to each chain. + +To find blocks, smoothxg applies a greedy algorithm that assumes that the graph +nodes are sorted according to their occurence in the graph's embedded paths. +The path-guided stochastic gradient descent based 1D sort implemented in +@command{odgi sort -Y} is designed to provide this kind of sort.") + (properties `((tunable? . #t))) + (license license:expat))) ;; TODO: Unbundle BBHash, parallel-hashmap, zstr (define-public graphaligner @@ -1665,19 +1961,30 @@ here}.") (define-public mummer (package (name "mummer") - (version "4.0.0beta2") + (version "4.0.0rc1") (source (origin (method url-fetch) (uri (string-append "https://github.com/mummer4/mummer/releases/" "download/v" version "/mummer-" version ".tar.gz")) (sha256 - (base32 - "14qvrmf0gkl4alnh8zgxlzmvwc027arfawl96i7jk75z33j7dknf")))) + (base32 "07bxw1vax1sai3g5xjn6sqngddlbnlabpqy373vw4fb55pdnl045")))) (build-system gnu-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'configure 'skip-test_md5-tests + (lambda _ + ;; There seems to be a bug with how these tests are called. + (substitute* "Makefile" + (("tests/mummer.sh") "") + (("tests/nucmer.sh") "") + (("tests/genome.sh") "") + (("tests/sam.sh") ""))))))) (inputs - `(("gnuplot" ,gnuplot) - ("perl" ,perl))) + (list gnuplot + perl)) (home-page "http://mummer.sourceforge.net/") (synopsis "Efficient sequence alignment of full genomes") (description "MUMmer is a versatil alignment tool for DNA and protein sequences.") @@ -1790,79 +2097,6 @@ reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.") (license license:expat))) -(define-public bh20-seq-resource - (let ((commit "2ae71911cd87ce4f2eabdff21e538267b3270d45") - (revision "4")) - (package - (name "bh20-seq-resource") - (version (git-version "1.0" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/pubseq/bh20-seq-resource") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1k6cc88hrcm77jwpdk2084q0zirv2vlbz3c07nmpbhk1lhqk5x0n")) - (modules '((guix build utils))) - (snippet - '(begin - (delete-file "gittaggers.py"))))) - (build-system python-build-system) - (arguments - (list - #:tests? #f ; Tests can't find pytest - #:phases - #~(modify-phases %standard-phases - (add-after 'unpack 'patch-program-calls - (lambda* (#:key inputs #:allow-other-keys) - (substitute* "bh20sequploader/qc_fasta.py" - (("\"minimap2\"") - (string-append "\"" (search-input-file - inputs "/bin/minimap2") - "\"")))))))) - (propagated-inputs - (list python-arvados-python-client - python-schema-salad - python-magic - python-pyshex - python-pyshexc-0.7 - python-py-dateutil - - ;; for the web - python-flask - python-pyyaml - python-redis - - ;; and for the service - python - gunicorn)) - (inputs - (list minimap2)) - (native-inputs - (list python-pytest-4 ; < 6 - python-pytest-runner-4)) ; < 5 - (home-page "https://github.com/pubseq/bh20-seq-resource") - (synopsis - "Tool to upload SARS-CoV-19 sequences and service to kick off analysis") - (description "This repository provides a sequence uploader for the -COVID-19 Virtual Biohackathon's Public Sequence Resource project. You can use -it to upload the genomes of SARS-CoV-2 samples to make them publicly and freely -available to other researchers.") - (license license:asl2.0)))) - -;; This version has no profile collisions. -(define-public bh20-seq-resource-for-service - (package - ;(inherit (fix-profile-collisions-for-bh20 bh20-seq-resource)) - (inherit - ((package-input-rewriting/spec - `(("python-google-api-core" . ,(const python-google-api-core-1)) - ("python-google-auth" . ,(const python-google-auth-1)) - ("python-pyparsing" . ,(const python-pyparsing-2.4.7)))) - bh20-seq-resource)) - (properties `((hidden? . #t))))) - (define-public python-scanpy-git (let ((commit "590d42309f9ed6550d7b887039990edfc1ac7648") ; April 22, 2020 (revision "1")) @@ -1903,32 +2137,60 @@ available to other researchers.") (delete-file "scanpy/tests/test_pca.py") #t))))))))) -;; TODO: Unbundle everything +;; TODO: Unbundle everything before upstreaming (define-public odgi (package (name "odgi") - (version "0.8.1") + (version "0.8.3") + (outputs '("out" "static")) (source (origin (method url-fetch) (uri (string-append "https://github.com/pangenome/odgi/releases" "/download/v" version "/odgi-v" version ".tar.gz")) (sha256 - (base32 "175083pb9hp0vn9a00hbxlayyk5a5j8p52yq5qfmbnfvndisbmbv")) + (base32 "1gw1xdb945z25rar6pba6kq5xdx8l7fkhxjyrvc1z1brva53p9hk")) (snippet #~(begin (use-modules (guix build utils)) (substitute* "CMakeLists.txt" (("-march=native") "") - (("-msse4\\.2") "")) - (delete-file-recursively "deps/pybind11") - (delete-file-recursively "deps/sdsl-lite"))))) + (("-msse4\\.2") "")))))) (build-system cmake-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'use-gnuinstalldirs-macros + (lambda _ + (substitute* "CMakeLists.txt" + (("project\\(odgi\\)" all) + (string-append all "\ninclude(GNUInstallDirs)")) + ;; This is different than the default. + ;(("PUBLIC_HEADER DESTINATION include/odgi") + ; "PUBLIC_HEADER DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}") + (("LIBRARY DESTINATION lib") + "LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}") + (("ARCHIVE DESTINATION lib") + "ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}")))) + (add-after 'unpack 'link-to-libodgi + (lambda _ + ;; This lets us provide libraries for different psABI levels. + (substitute* "CMakeLists.txt" + (("^ \\$<TARGET_OBJECTS:odgi_objs>.*") "") + (("target_link_libraries\\(odgi " all) + (string-append all "libodgi_shared "))))) + (add-after 'install 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (mkdir-p (string-append #$output:static "/lib")) + (rename-file (string-append #$output "/lib/libodgi.a") + (string-append #$output:static "/lib/libodgi.a"))))))) (native-inputs (list pkg-config)) (inputs (list jemalloc libdivsufsort + openmpi pybind11 python sdsl-lite)) @@ -1953,189 +2215,280 @@ in-memory footprint at the cost of packing and unpacking.") (properties '((tunable? . #t))) (license license:expat))) +(define-public odgi-x86-64-v2 + (package/inherit odgi + (name "odgi-x86-64-v2") + (arguments + (substitute-keyword-arguments (package-arguments odgi) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v2" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v2" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v2")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")) + (delete-file-recursively (string-append #$output "/include")))) + (replace 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v2/libodgi.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +(define-public odgi-x86-64-v3 + (package/inherit odgi + (name "odgi-x86-64-v3") + (arguments + (substitute-keyword-arguments (package-arguments odgi) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v3" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v3" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v3")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")) + (delete-file-recursively (string-append #$output "/include")))) + (replace 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v3/libodgi.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +(define-public odgi-x86-64-v4 + (package/inherit odgi + (name "odgi-x86-64-v4") + (arguments + (substitute-keyword-arguments (package-arguments odgi) + ((#:configure-flags flags #~'()) + #~(append (list "-DEXTRA_FLAGS=-march=x86-64-v4" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v4" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v4")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")) + (delete-file-recursively (string-append #$output "/include")))) + (replace 'move-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v4/libodgi.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (rename-file (string-append #$output lib) + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +;; This copy of odgi will automatically use the libraries that target the +;; x86_64 psABI which the hardware supports. +(define-public odgi-hwcaps + (package/inherit odgi + (name "odgi-hwcaps") + (arguments + (substitute-keyword-arguments (package-arguments odgi) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'install-optimized-libraries + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((hwcaps "/lib/glibc-hwcaps")) + (copy-recursively + (string-append (assoc-ref inputs "odgi-x86-64-v2") + hwcaps "/x86-64-v2") + (string-append #$output hwcaps "/x86-64-v2")) + (copy-recursively + (string-append (assoc-ref inputs "odgi-x86-64-v3") + hwcaps "/x86-64-v3") + (string-append #$output hwcaps "/x86-64-v3")) + (copy-recursively + (string-append (assoc-ref inputs "odgi-x86-64-v4") + hwcaps "/x86-64-v4") + (string-append #$output hwcaps "/x86-64-v4"))))))))) + (native-inputs + (modify-inputs (package-native-inputs odgi) + (append odgi-x86-64-v2 + odgi-x86-64-v3 + odgi-x86-64-v4))) + (properties `((tunable? . #f))))) + (define-public vg (package (name "vg") - (version "1.39.0") + (version "1.50.0") (source (origin (method url-fetch) (uri (string-append "https://github.com/vgteam/vg/releases/download/v" version "/vg-v" version ".tar.gz")) (sha256 - (base32 "0cj575qr2jkingrm6r4ki7f89s7glrf18d4pvaa69smxh2vbajv3")) - (modules '((guix build utils))) + (base32 "1n06fh6qvffhbxy7m096r8cy16wi0nm6gfgi3rsjy9zrb7g1jzhs")) (snippet - '(begin - ;; List all the options, makes it easier to try to remove them. - ;(delete-file-recursively "deps/BBHash") - ;(delete-file-recursively "deps/DYNAMIC") - ;(delete-file-recursively "deps/FlameGraph") - ;(delete-file-recursively "deps/atomic_queue") - ;(delete-file-recursively "deps/backward-cpp") - (delete-file-recursively "deps/bash-tap") - ;(delete-file-recursively "deps/dozeu") - (delete-file-recursively "deps/elfutils") - (delete-file-recursively "deps/fastahack") - ;(delete-file-recursively "deps/fermi-lite") - ;(delete-file-recursively "deps/gbwt") - ;(delete-file-recursively "deps/gbwtgraph") - ;(delete-file-recursively "deps/gcsa2") - ;(delete-file-recursively "deps/gfakluge") - ;(delete-file-recursively "deps/gssw") - (delete-file-recursively "deps/htslib") - ;(delete-file-recursively "deps/ips4o") - (delete-file-recursively "deps/jemalloc") - ;(delete-file-recursively "deps/libVCFH") - ;(delete-file-recursively "deps/libbdsg") - ;(delete-file-recursively "deps/libbdsg/bdsg/deps") - (delete-file-recursively "deps/libbdsg/bdsg/deps/BBHash") - (delete-file-recursively "deps/libbdsg/bdsg/deps/DYNAMIC") - ;(delete-file-recursively "deps/libbdsg/bdsg/deps/DYNAMIC/deps/hopscotch-map") - ;(delete-file-recursively "deps/libbdsg/bdsg/deps/hopscotch-map") - (delete-file-recursively "deps/libbdsg/bdsg/deps/libhandlegraph") - ;(delete-file-recursively "deps/libbdsg/bdsg/deps/mio") - (delete-file-recursively "deps/libbdsg/bdsg/deps/pybind11") - (delete-file-recursively "deps/libbdsg/bdsg/deps/sdsl-lite") - (delete-file-recursively "deps/libbdsg/bdsg/deps/sparsepp") - ;(delete-file-recursively "deps/libdeflate") - ;(delete-file-recursively "deps/libhandlegraph") - ;(delete-file-recursively "deps/libVCFH") - ;(delete-file-recursively "deps/libvgio") - ;(delete-file-recursively "deps/libvgio/deps") ; libhandlegraph - ;(delete-file-recursively "deps/lru_cache") - ;(delete-file-recursively "deps/mio") - ;(delete-file-recursively "deps/mmmultimap") - (delete-file-recursively "deps/mmmultimap/deps/DYNAMIC") - (delete-file-recursively "deps/mmmultimap/deps/args") - (delete-file-recursively "deps/mmmultimap/deps/atomic_queue") - ;(delete-file-recursively "deps/mmmultimap/deps/hopscotch-map") - (delete-file-recursively "deps/mmmultimap/deps/ips4o") - (delete-file-recursively "deps/mmmultimap/deps/mio") - ;(delete-file-recursively "deps/mmmultimap/deps/paryfor") - (delete-file-recursively "deps/mmmultimap/deps/sdsl-lite") - ;(delete-file-recursively "deps/pinchesAndCacti") - ;(delete-file-recursively "deps/progress_bar") - (delete-file-recursively "deps/raptor") - ;(delete-file-recursively "deps/sdsl-lite") - ;(delete-file-recursively "deps/sha1") - (delete-file-recursively "deps/snappy") - ;(delete-file-recursively "deps/sonLib") - (delete-file-recursively "deps/sparsehash") - ;(delete-file-recursively "deps/sparsepp") - ;(delete-file-recursively "deps/ssw") - ;(delete-file-recursively "deps/structures") - ;(delete-file-recursively "deps/sublinear-Li-Stephens") - (delete-file-recursively "deps/sublinear-Li-Stephens/deps") - (delete-file-recursively "deps/tabixpp") - (delete-file-recursively "deps/vcflib") - ;(delete-file-recursively "deps/xg") - (delete-file-recursively "deps/xg/deps") - ;; libvgio doesn't search the correct include directory. - (copy-recursively "deps/libhandlegraph/src/include/handlegraph" - "deps/libvgio/include/handlegraph"))))) + #~(begin + (use-modules (guix build utils)) + (substitute* (find-files "." "(CMakeLists\\.txt|Makefile)") + (("-march=native") "") + (("-mtune=native") "") + (("-msse4.2") "") + (("-mcx16") "")))))) (build-system gnu-build-system) (arguments `(#:phases (modify-phases %standard-phases (delete 'configure) ; no configure script - ,@(if (target-riscv64?) - ;; riscv64 doesn't take '-march=native. This needs to be removed - ;; for all architectures if/when vg is upstreamed. - `((add-after 'unpack 'dont-build-native - (lambda _ - (substitute* (append (find-files "." "CMakeLists\\.txt") - (find-files "." "Makefile")) - (("-march=native") ""))))) - '()) (add-after 'unpack 'patch-source (lambda* (#:key inputs #:allow-other-keys) + ;; Most of these are so that we can skip bootstrapping some of the sources. (substitute* "Makefile" ;; PKG_CONFIG_DEPS needs to be substituted to actually link to everything. - (("cairo jansson") - "cairo htslib jansson libdw libelf protobuf raptor2 sdsl-lite tabixpp vcflib") + (("cairo libzstd") + "cairo htslib libzstd libdw libelf protobuf raptor2 sdsl-lite tabixpp vcflib fastahack libdeflate") ;; Skip the part where we link static libraries special. It doesn't like the changes we make (("-Wl,-B.*") "\n") (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libtabixpp\\.a") "$(LIB_DIR)/libtabixpp.a") ((" \\$\\(LIB_DIR\\)/libtabixpp\\.a") - (string-append " " (assoc-ref inputs "tabixpp") "/lib/libtabixpp.so")) + (string-append " " (search-input-file inputs "/lib/libtabixpp.so"))) (("\\$\\(LIB_DIR\\)/pkgconfig/tabixpp\\.pc") - (string-append " " (assoc-ref inputs "tabixpp") "/lib/pkgconfig/tabixpp.pc")) + (string-append " " (search-input-file inputs "/lib/pkgconfig/tabixpp.pc"))) (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libhts\\.a") "$(LIB_DIR)/libhts.a") ((" \\$\\(LIB_DIR\\)/libhts\\.a") - (string-append " " (assoc-ref inputs "htslib") "/lib/libhts.so")) + (string-append " " (search-input-file inputs "/lib/libhts.so"))) (("\\$\\(LIB_DIR\\)/pkgconfig/htslib\\.pc") - (string-append " " (assoc-ref inputs "htslib") "/lib/pkgconfig/htslib.pc")) + (string-append " " (search-input-file inputs "/lib/pkgconfig/htslib.pc"))) + + (("\\$\\(CWD\\)/\\$\\(LIB_DIR\\)/libdeflate\\.a") "$(LIB_DIR)/libdeflate.a") + ((" \\$\\(LIB_DIR\\)/libdeflate\\.a") + (string-append " " (search-input-file inputs "/lib/libdeflate.so"))) ((" \\$\\(LIB_DIR\\)/libvcflib.a") - (string-append " " (assoc-ref inputs "vcflib") "/lib/libvcflib.so")) + (string-append " " (search-input-file inputs "/lib/libvcflib.so"))) ((" \\$\\(BIN_DIR\\)/vcf2tsv") - (string-append " " (assoc-ref inputs "vcflib") "/bin/vcf2tsv")) - ((" \\$\\(VCFLIB_DIR\\)/bin/vcf2tsv") - (string-append " " (assoc-ref inputs "vcflib") "/bin/vcf2tsv")) + (string-append " " (search-input-file inputs "/bin/vcf2tsv"))) ((" \\$\\(FASTAHACK_DIR\\)/fastahack") - (string-append " " (assoc-ref inputs "fastahack") "/bin/fastahack")) - ((" \\$\\(FASTAHACK_DIR\\)/bin/fastahack") - (string-append " " (assoc-ref inputs "fastahack") "/bin/fastahack")) + (string-append " " (search-input-file inputs "/bin/fastahack"))) (("\\+= \\$\\(OBJ_DIR\\)/Fasta\\.o") - (string-append "+= " (assoc-ref inputs "fastahack") "/lib/libfastahack.so")) + (string-append "+= " (search-input-file inputs "/lib/libfastahack.so"))) ((" \\$\\(LIB_DIR\\)/libsnappy.a") - (string-append " " (assoc-ref inputs "snappy") "/lib/libsnappy.so")) + (string-append " " (search-input-file inputs "/lib/libsnappy.so"))) ;; Only link against the libraries in the elfutils package. (("-ldwfl -ldw -ldwelf -lelf -lebl") "-ldw -lelf") ((" \\$\\(LIB_DIR\\)/libelf.a") - (string-append " " (assoc-ref inputs "elfutils") "/lib/libelf.so")) + (string-append " " (search-input-file inputs "/lib/libelf.so"))) ((" \\$\\(LIB_DIR\\)/libdw.a") - (string-append " " (assoc-ref inputs "elfutils") "/lib/libdw.so")) + (string-append " " (search-input-file inputs "/lib/libdw.so"))) ;; We need the Make.helper file in SDSL_DIR for gcsa2 ;((" \\$\\(LIB_DIR\\)/libsdsl.a") - ; (string-append " " (assoc-ref inputs "sdsl-lite") "/lib/libsdsl.so")) + ; (string-append " " (search-input-file inputs "/lib/libsdsl.so"))) + ((" \\$\\(LIB_DIR\\)/%divsufsort.a") + (string-append " " (dirname + (search-input-file inputs "/lib/libdivsufsort.so")) + "%divsufsort.so")) ((" \\$\\(LIB_DIR\\)/libdivsufsort.a") - (string-append " " (assoc-ref inputs "libdivsufsort") "/lib/libdivsufsort.so")) + (string-append " " (search-input-file inputs "/lib/libdivsufsort.so"))) + ((" \\$\\(LIB_DIR\\)/%divsufsort64.a") + (string-append " " (dirname + (search-input-file inputs "/lib/libdivsufsort64.so")) + "%divsufsort64.so")) ((" \\$\\(LIB_DIR\\)/libdivsufsort64.a") - (string-append " " (assoc-ref inputs "libdivsufsort") "/lib/libdivsufsort64.so")) + (string-append " " (search-input-file inputs "/lib/libdivsufsort64.so"))) ((" \\$\\(LIB_DIR\\)/libjemalloc.a") - (string-append " " (assoc-ref inputs "jemalloc") "/lib/libjemalloc.a")) + (string-append " " (search-input-file inputs "/lib/libjemalloc.a"))) ((" \\$\\(INC_DIR\\)/sparsehash") - (string-append " " (assoc-ref inputs "sparsehash") "/include/sparsehash")) + (string-append " " (search-input-directory inputs "/include/sparsehash"))) ((" \\$\\(INC_DIR\\)/raptor2") - (string-append " " (assoc-ref inputs "raptor2") "/include/raptor2")) + (string-append " " (search-input-directory inputs "/include/raptor2"))) ((" \\$\\(LIB_DIR\\)/libraptor2.a") - (string-append " " (assoc-ref inputs "raptor2") "/lib/libraptor2.so")) + (string-append " " (search-input-file inputs "/lib/libraptor2.so"))) ((" \\$\\(BIN_DIR\\)/rapper") - (string-append " " (assoc-ref inputs "raptor2") "/bin/rapper"))) - ;; vcf2tsv shows up in a couple of other places - (substitute* "test/t/02_vg_construct.t" - (("../deps/vcflib/bin/vcf2tsv") (which "vcf2tsv"))))) - (add-after 'unpack 'fix-fastahack-dependency + (string-append " " (search-input-file inputs "/bin/rapper")))))) + (add-after 'unpack 'link-with-some-shared-libraries + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("deps/mmmultimap/CMakeLists.txt" + "deps/xg/CMakeLists.txt" + "deps/xg/deps/mmmulti/CMakeLists.txt") + (("\".*libsdsl\\.a\"") "\"-lsdsl\"") + (("\".*libdivsufsort\\.a\"") "\"-ldivsufsort\"") + (("\".*libdivsufsort64\\.a\"") "\"-ldivsufsort64\"") + (("\\$\\{sdsl-lite_INCLUDE\\}") + (search-input-directory inputs "/include/sdsl")) + (("\\$\\{sdsl-lite-divsufsort_INCLUDE\\}") + (dirname + (search-input-file inputs "/include/divsufsort.h")))))) + #; + (add-before 'patch-source 'use-shared-libvg + (lambda* (#:key inputs outputs #:allow-other-keys) + (substitute* "Makefile" + (("libvg\\.a") "libvg.so") + ;; Have the linker find the shared library. + (("\\$\\(LIB_DIR\\)/libvg.\\$\\(SHARED_SUFFIX\\) \\$\\(LDFLAGS\\)") + "-lvg $(LDFLAGS)") + (("\\$\\(LDFLAGS\\) \\$\\(LIB_DIR\\)/libvg.so") + "$(LDFLAGS) -lvg")) + (setenv "LDFLAGS" (string-append "-Wl,-rpath=" + (assoc-ref outputs "out") "/lib")) + + ;; We need to tell a number of dependencies to build with -fPIC. + (substitute* "Makefile" + (("^CXXFLAGS := -O3") + (string-append "CFLAGS := -fPIC\n" + "CXXFLAGS := -O3 -fPIC")) + (("^export CXXFLAGS") + (string-append "export CFLAGS\n" + "$(info CFLAGS are $(CFLAGS))\n" + "export CXXFLAGS")) + ((" \\$\\(LIB_DIR\\)/libjemalloc.a") + (string-append " " (assoc-ref inputs "jemalloc") + "/lib/libjemalloc_pic.a"))) + ;; We don't want to pull in all the global CXXFLAGS here. + (substitute* "deps/sublinear-Li-Stephens/makefile" + (("^CXXFLAGS:=") "CXXFLAGS:= -fPIC ")) + ;; CMAKE_CXX_FLAGS aren't set globally. + (substitute* "deps/kff-cpp-api/CMakeLists.txt" + (("CMAKE_CXX_FLAGS \"") "CMAKE_CXX_FLAGS \" -fPIC ")))) + (add-after 'unpack 'dont-build-shared-vgio (lambda _ - (substitute* "src/aligner.hpp" - (("Fasta.h") "fastahack/Fasta.h")))) - (add-after 'unpack 'fix-hopscotch-dependency + ;; vg will link with libvgio and fail the 'validate-runpath phase. + (substitute* "deps/libvgio/CMakeLists.txt" + (("TARGETS vgio vgio_static") "TARGETS vgio_static")))) + (add-after 'unpack 'fix-fastahack-dependency (lambda _ - (substitute* "Makefile" - ;; The build directory for hopscotch_map-prefix. - (("rm -Rf build && ") "")) - ;; Don't try to download hopscotch_map from the internet. - (substitute* "deps/DYNAMIC/CMakeLists.txt" - ((".*GIT_REPOSITORY.*") - "SOURCE_DIR \"../../libbdsg/bdsg/deps/hopscotch-map\"\n") - ((".*BUILD_IN_SOURCE.*") "")) - ;; We still need to copy it to the expected location. - (copy-recursively - "deps/libbdsg/bdsg/deps/hopscotch-map" - "deps/DYNAMIC/build/hopscotch_map-prefix/src/hopscotch_map"))) + (substitute* (append (list "src/aligner.hpp" + "src/vg.hpp") + (find-files "deps/vcflib/src" "\\.cpp$")) + (("Fasta.h") "fastahack/Fasta.h")) + (substitute* '("deps/vcflib/src/Variant.h" + "src/constructor.hpp" + "src/index_registry.cpp") + (("<Fasta.h>") "\"fastahack/Fasta.h\"")))) (add-after 'unpack 'adjust-tests (lambda* (#:key inputs #:allow-other-keys) (let ((bash-tap (assoc-ref inputs "bash-tap"))) @@ -2144,13 +2497,25 @@ in-memory footprint at the cost of packing and unpacking.") (string-append "BASH_TAP_ROOT=" bash-tap "/bin\n")) ((".*bash-tap-bootstrap") (string-append ". " bash-tap "/bin/bash-tap-bootstrap"))) - ;; Lets skip the 4 failing tests for now. They fail with our + (substitute* "test/t/02_vg_construct.t" + (("../deps/fastahack/fastahack") (which "fastahack")) + (("../bin/vcf2tsv") (which "vcf2tsv"))) + ;; Lets skip the 9 failing tests for now. They fail with our ;; bash-tap and the bundled one. (substitute* "test/t/02_vg_construct.t" - ((".*the graph contains.*") "is $(true) \"\" \"\"\n")) + ((".*self-inconsistent.*") "is $(true) \"\" \"\"\n")) + (substitute* "test/t/07_vg_map.t" + ;; Change in fasta's output + (("identity\\) 1 \"") "identity) 1.0 \"")) (substitute* '("test/t/07_vg_map.t" "test/t/33_vg_mpmap.t") ((".*node id.*") "is $(true) \"\" \"\"\n")) + (substitute* "test/t/48_vg_convert.t" + (("true \"vg.*") "true \"true\"\n")) + (substitute* "test/t/50_vg_giraffe.t" + ((".*A long read can.*") "is $(true) \"\" \"\"\n") + ((".*A long read has.*") "is $(true) \"\" \"\"\n") + ((".*Long read minimizer.*") "is $(true) \"\" \"\"\n")) ;; Don't test the docs, we're not providing npm (substitute* "Makefile" ((".*test-docs.*") ""))))) @@ -2162,47 +2527,50 @@ in-memory footprint at the cost of packing and unpacking.") (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (install-file "bin/vg" (string-append out "/bin")) - (install-file "lib/libvg.a" (string-append out "/lib")) + ;(install-file "lib/libvg.so" (string-append out "/lib")) (for-each (lambda (file) (install-file file (string-append out "/share/man/man1"))) (find-files "doc/man" "\\.1$")))))) #:test-target "test")) (native-inputs - `(,@(if (member (%current-system) - (package-transitive-supported-systems ruby-asciidoctor)) - `(("asciidoctor" ,ruby-asciidoctor)) - '()) - ("bash-tap" ,bash-tap) - ("bc" ,bc) - ("cmake" ,cmake-minimal) - ("jq" ,jq) - ("perl" ,perl) - ("pkg-config" ,pkg-config) - ("samtools" ,samtools) - ("util-linux" ,util-linux) - ("which" ,which) - ("xxd" ,xxd))) + (append + (if (supported-package? ruby-asciidoctor) + (list ruby-asciidoctor) + '()) + (list bash-tap + bc + cmake-minimal + jq + perl + pkg-config + samtools + util-linux + which + xxd))) (inputs - `(("boost" ,boost) - ("cairo" ,cairo) - ("curl" ,curl) - ("elfutils" ,elfutils) - ("fastahack" ,fastahack) - ("htslib" ,htslib) - ("jansson" ,jansson) - ("jemalloc" ,jemalloc) - ("libdivsufsort" ,libdivsufsort) - ("ncurses" ,ncurses) - ("protobuf" ,protobuf) - ("raptor2" ,raptor2) - ("sdsl-lite" ,sdsl-lite) - ("smithwaterman" ,smithwaterman) - ("snappy" ,snappy) - ("sparsehash" ,sparsehash) - ("tabixpp" ,tabixpp) - ("vcflib" ,vcflib) - ("zlib" ,zlib))) + (list boost + cairo + curl + elfutils + fastahack + htslib + jansson + jemalloc + libdeflate + libdivsufsort + ncurses + openmpi + protobuf + raptor2 + sdsl-lite + smithwaterman + snappy + sparsehash + tabixpp + vcflib + zlib + (list zstd "lib"))) (home-page "https://www.biostars.org/t/vg/") (synopsis "Tools for working with genome variation graphs") (description "Variation graphs provide a succinct encoding of the sequences @@ -2216,7 +2584,8 @@ gene models and transcripts) as walks through nodes connected by edges @end enumerate This model is similar to sequence graphs that have been used in assembly and multiple sequence alignment.") - (properties `((release-monitoring-url . "https://github.com/vgteam/vg/releases"))) + (properties `((release-monitoring-url . "https://github.com/vgteam/vg/releases") + (tunable? . #t))) (license (list license:expat ; main program @@ -2227,6 +2596,162 @@ multiple sequence alignment.") license:zlib ; deps/sonLib/externalTools/cutest license:boost1.0)))) ; catch.hpp +(define-public pggb + (let ((commit "9ebff27320382e470ed38a85b4448402e1e7c353") + (revision "1")) + (package + (name "pggb") + (version (git-version "0.5.1" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/pangenome/pggb") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0rgpj52q3ai7f1saqbilgx5gz4f403x3427wq649qwv84ivmi1sf")))) + (build-system copy-build-system) + (arguments + (list + #:install-plan + #~'(("pggb" "bin/") + ("partition-before-pggb" "bin/") + ("scripts/" "bin/") + ("scripts" "bin/scripts")) + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'force-python3 + (lambda _ + (substitute* (find-files "scripts" "\\.py$") + (("/usr/bin/python") "/usr/bin/python3")))) + (add-before 'install 'patch-and-wrap-scripts + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "scripts/vcf_preprocess.sh" + (("bcftools ") + (string-append (search-input-file inputs "/bin/bcftools") " "))) + (wrap-script "scripts/net2communities.py" + `("GUIX_PYTHONPATH" ":" prefix + (,(getenv "GUIX_PYTHONPATH")))))) + (add-after 'install 'wrap-scripts + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (for-each + (lambda (file) + (wrap-script file + `("R_LIBS_SITE" ":" prefix + (,(getenv "R_LIBS_SITE"))) + `("PATH" ":" prefix + ,(map (lambda (input) (string-append input "/bin")) + '#$(map (lambda (label) + (or (this-package-input (string-append label "-hwcaps")) + (this-package-input label))) + (list "bc" + "bcftools" + "bedtools" + "gfaffix" + "htslib" + "fastix" + "multiqc" + "mummer" + "odgi" + "pafplot" + "parallel" + "pigz" + "python" + "r-data-table" + "r-minimal" + "rtg-tools" + "samtools" + "seqwish" + "smoothxg" + "time" + "vcfbub" + "vcflib" + "vg" + "wfmash")))))) + (list (string-append out "/bin/pggb") + (string-append out "/bin/partition-before-pggb") + (string-append out "/bin/gfa2evaluation.sh") + (string-append out "/bin/scripts/gfa2evaluation.sh")))))) + (add-after 'install 'substitute-file-paths + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (substitute* (string-append out "/bin/gfa2evaluation.sh") + (("/usr/local/bin/vcf_preprocess.sh") + (string-append out "/bin/vcf_preprocess.sh")) + (("/usr/local/bin/nucmer2vcf.R") + (string-append out "/bin/nucmer2vcf.R"))))))))) + (inputs + (list bc + bcftools + bedtools + gfaffix + guile-3.0 ; for wrap-script + htslib ; tabix + fastix + multiqc + mummer + odgi + pafplot + parallel + pigz + python + python-igraph + r-data-table + r-minimal + rtg-tools + samtools + seqwish + smoothxg + time + vcfbub + vcflib + vg + wfmash)) + (home-page "https://doi.org/10.1101/2023.04.05.535718") + (synopsis "PanGenome Graph Builder") + (description "@command{pggb} builds +@url{https://doi.org/10.1146%2Fannurev-genom-120219-080406, pangenome} +@url{https://doi.org/10.1038/nbt.4227, variation graphs} from a set of input +sequences. +A pangenome variation graph is a kind of generic multiple sequence alignment. +It lets us understand any kind of sequence variation between a collection of +genomes. It shows us similarity where genomes walk through the same parts of +the graph, and differences where they do not. +@command{pggb} generates this kind of graph using an all-to-all alignment of +input sequences (@url{https://github.com/waveygang/wfmash, wfmash}), graph +induction (@url{https://doi.org/10.1101/2022.02.14.480413, seqwish}), and +progressive normalization (@url{https://github.com/pangenome/smoothxg, +smoothxg}, @url{https://github.com/marschall-lab/GFAffix, gfaffix}). After +construction, @command{pggb} generates diagnostic visualizations of the graph +(@url{https://doi.org/10.1093/bioinformatics/btac308, odgi}). A variant call +report (in VCF) representing both small and large variants can be generated +based on any reference genome included in the graph +(@url{https://github.com/vgteam/vg, vg}). @command{pggb} writes its output in +@url{https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md, GFAv1} format, +which can be used as input by numerous \"genome graph\" and pangenome tools, +such as the @url{https://github.com/vgteam/vg, vg} and +@url{https://doi.org/10.1093/bioinformatics/btac308, odgi} toolkits. +@command{pggb} has been tested at scale in the @acronym{Human Pangenome +Reference Consortium, HPRC} as a method to build a graph from the +@url{https://doi.org/10.1101/2022.07.09.499321, draft human pangenome}.") + (license license:expat)))) + +(define use-glibc-hwcaps + (package-input-rewriting/spec + ;; Replace some packages with ones built targeting custom packages build + ;; with glibc-hwcaps support. + `(;("gsl" . ,(const gsl-hwcaps)) ; Causes too many rebuilds through multiqc + ("sdsl-lite" . ,(const sdsl-lite-hwcaps)) + ("seqwish" . ,(const seqwish-hwcaps)) + ("odgi" . ,(const odgi-hwcaps)) + ("wfmash" . ,(const wfmash-hwcaps))))) + +(define-public pggb-with-hwcaps + (package + (inherit (use-glibc-hwcaps pggb)) + (name "pggb-with-hwcaps"))) + (define-public ucsc-genome-browser (package (name "ucsc-genome-browser") @@ -3936,3 +4461,200 @@ automatically vectorize for different architectures without adapting the code.") (substitute-keyword-arguments (package-arguments wfa2-lib) ((#:make-flags flags ''()) #~(cons "CC_FLAGS+=-static" #$flags)))))) + +(define-public r-rrbgen + (package + (name "r-stitch") + (version "0.0.6") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/rwdavies/rrbgen/releases/download/" + version "/rrbgen_" version ".tar.gz")) + (sha256 + (base32 + "1vhqy8licl2pkzar4aag0q5fhnb3fdch8acyjh9445ia42z01z9c")))) + (build-system r-build-system) + (propagated-inputs + (list r-rcpp + r-rcpparmadillo)) + (home-page "https://github.com/rwdavies/rrbgen") + (synopsis "Lightweight limited functionality R bgen read/write library") + (description "@code{r-rrbgen} supports v1.3 of the bgen format. It supports reading +and writing using 8, 16, 24 or 32 bits per probability, using Layout = +2 and CompressedSNPBlocks = 1, for bi-allelic SNPs with samples of +ploidy 2. Any other format specification may crash unexpectedly +without a properly defined error.") + (license license:gpl3))) + +(define-public seqlib + (package + (name "seqlib") + (version "0.1.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Zilong-Li/SeqLib") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1hczg1swghnxm6af74l09crdgf7l282jabmyck9mi5bk6vg9s1pn")))) + (build-system gnu-build-system) + (arguments + (list #:phases + #~(modify-phases %standard-phases + ;; Patch build scripts to unbundle htslib and build a + ;; seqlib shared library using libtool. + (add-after 'unpack 'patch-build-scripts + (lambda _ + ;; Initialize libtool. + (substitute* "configure.ac" + (("AM_INIT_AUTOMAKE\\(foreign\\)\n" all) + (string-append all "LT_INIT\n"))) + (substitute* "Makefile.am" + ;; Install headers + (("^SUBDIRS" all) + (string-append "nobase_include_HEADERS = " + (string-join (find-files "SeqLib")) + "\n" all)) + ;; Do not recurse into htslib submodule. + (("htslib") "") + ;; Remove install target override. + (("^install:") "") + (("^\tmkdir -p lib && cp src/libseqlib.a /libhts.a lib") "")) + (substitute* "src/Makefile.am" + ;; Build libtool library. + (("noinst_LIBRARIES = libseqlib\\.a") + "lib_LTLIBRARIES = libseqlib.la\nlibseqlib_la_LIBADD = -ljsoncpp") + (("libseqlib\\.a") "libseqlib.la") + (("libseqlib_a") "libseqlib_la")) + (substitute* (list "SeqLib/BamHeader.h" + "SeqLib/BamRecord.h" + "SeqLib/RefGenome.h" + "src/ReadFilter.cpp") + ;; Patch path to htslib headers. + (("\"htslib/htslib/([^\"]*)\"" all header) + (string-append "<htslib/" header ">")))))))) + (inputs + (list zlib)) + (native-inputs + (list autoconf automake libtool)) + ;; seqlib headers include headers from htslib and jsoncpp. So, + ;; they are propagated inputs. + (propagated-inputs + (list htslib jsoncpp)) + (home-page "https://github.com/Zilong-Li/SeqLib") + (synopsis "C++ htslib interface for manipulating sequence data and VCF") + (description "@code{seqlib} is a C++ htslib interface for manipulating sequence data +and VCF files.") + (license (list license:expat ; SeqLib/IntervalTree.h, SeqLib/aho_corasick.hpp, + ; json/json-forwards.h, json/json.h, src/jsoncpp.cpp, src/ssw.c, + license:asl2.0)))) ; main license + +(define-public vcfpp + (package + (name "vcfpp") + (version "0.3.3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/Zilong-Li/vcfpp/releases/download/v" + version "/vcfpp.h")) + (sha256 + (base32 + "1wq76wz81y09ic37z30vljqnczhwx2qijav0nfvg6xi8wd2c75n3")))) + (build-system copy-build-system) + (arguments + (list #:install-plan #~'(("vcfpp.h" "include/vcfpp/vcfpp.h")))) + (home-page "https://github.com/Zilong-Li/vcfpp") + (synopsis "C++ API of htslib") + (description "@code{vcfpp} is a single C++ file as +interface to the basic htslib. It can be easily included in a C++ +program for scripting high-performance genomic analyses.") + (license license:asl2.0))) + +(define-public r-stitch + (package + (name "r-stitch") + (version "1.6.10") + (source + ;; The release tarball bundles dependencies. So, use git-fetch. + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/rwdavies/STITCH") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0iy5fq2l5a35xdxqaf9ypj56da57qmwppwqmh9nflbvmbc7kgbkf")))) + (build-system r-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "STITCH"))) + (add-after 'chdir 'patch-build-system + (lambda _ + (substitute* "src/Makevars" + (("\\$\\(SEQLIB_ROOT\\)/src/libseqlib.a") "-lseqlib") + (("\\$\\(SEQLIB_ROOT\\)/htslib/libhts.a") "-lhts") + ((": SeqLib") ":"))))))) + (inputs + (list curl htslib seqlib zlib)) + (native-inputs + (list autoconf automake vcfpp)) + (propagated-inputs + (list r-data-table r-rrbgen + ;; FIXME: These should be inputs that are substituted into + ;; the source. But, for some reason, the reference scanner + ;; does not pick them up that way. + coreutils findutils htslib rsync)) + (home-page "https://github.com/rwdavies/STITCH") + (synopsis "Sequencing to imputation through constructing haplotypes") + (description "@code{r-stitch} is an R program for reference panel free, +read aware, low coverage sequencing genotype imputation. STITCH runs +on a set of samples with sequencing reads in BAM format, as well as a +list of positions to genotype, and outputs imputed genotypes in VCF +format.") + (license license:gpl3))) + +(define-public hifiasm + (package + (name "hifiasm") + (version "0.19.8") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/chhylp123/hifiasm") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1g6m2qdc0224vjaic87669g7y9ky1yps07qbjkmbh1vakz4zmgvr")))) + (build-system gnu-build-system) + (arguments + (list #:tests? #f + #:phases + #~(modify-phases %standard-phases + (delete 'configure) + (replace 'install + (lambda _ + (install-file "hifiasm" (string-append #$output "/bin")) + (install-file "hifiasm.1" (string-append #$output "/share/man/man1"))))))) + (inputs + (list zlib)) + (home-page "https://github.com/chhylp123/hifiasm") + (synopsis "haplotype-resolved assembler for accurate Hifi reads") + (description "Hifiasm is a fast haplotype-resolved de-novo assembler originally +designed for PacBio HiFi reads. Its latest release supports the +telomere-to-telomere assembly by utilizing ultralong Oxford Nanopore +reads. Hifiasm produces arguably the best single-sample +telomere-to-telomere assemblies combing HiFi, ultralong and Hi-C +reads, and it is one of the best haplotype-resolved assemblers for the +trio-binning assembly given parental short reads. For a human genome, +hifiasm can produce the telomere-to-telomere assembly in one day.") + (license license:expat))) diff --git a/gn/packages/crates-io.scm b/gn/packages/crates-io.scm index e500d86..4cebb33 100644 --- a/gn/packages/crates-io.scm +++ b/gn/packages/crates-io.scm @@ -7,9 +7,35 @@ #:use-module (guix build-system cargo) #:use-module (gnu packages crates-graphics) #:use-module (gnu packages crates-io) + #:use-module (gnu packages crates-windows) #:use-module (gnu packages maths) #:use-module (gnu packages python)) +(define-public rust-assert-cmd-0.12 + (package + (name "rust-assert-cmd") + (version "0.12.2") + (source (origin + (method url-fetch) + (uri (crate-uri "assert-cmd" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1xfn2spazxk3ljj9q3250a24gndja9vwa0h0rnbccdrbd4ncyvwk")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-doc-comment" ,rust-doc-comment-0.3) + ("rust-escargot" ,rust-escargot-0.5) + ("rust-predicates" ,rust-predicates-1) + ("rust-predicates-core" ,rust-predicates-core-1) + ("rust-predicates-tree" ,rust-predicates-tree-1) + ("rust-wait-timeout" ,rust-wait-timeout-0.2)))) + (home-page "https://github.com/assert-rs/assert_cmd") + (synopsis "Test CLI Applications.") + (description "Test CLI Applications.") + (license (list license:expat license:asl2.0)))) + (define-public rust-bgzip-0.2 (package (name "rust-bgzip") @@ -66,25 +92,6 @@ for massive key sets}. It generates an @acronym{MPHF, minimal perfect hash functions} for a collection of hashable objects.") (license license:expat))) -(define-public rust-clap-lex-0.3 - (package - (name "rust-clap-lex") - (version "0.3.0") - (source (origin - (method url-fetch) - (uri (crate-uri "clap-lex" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1a4dzbnlxiamfsn0pnkhn7n9bdfjh66j9fxm6mmr7d227vvrhh8d")))) - (build-system cargo-build-system) - (arguments - `(#:cargo-inputs (("rust-os-str-bytes" ,rust-os-str-bytes-6)))) - (home-page "https://github.com/clap-rs/clap/tree/master/clap_lex") - (synopsis "Minimal, flexible command line parser") - (description "Minimal, flexible command line parser") - (license (list license:expat license:asl2.0)))) - (define-public rust-cuckoofilter-0.5 (package (name "rust-cuckoofilter") @@ -144,7 +151,7 @@ functions} for a collection of hashable objects.") "Library for working with graphs in the GFA (Graphical Fragment Assembly) format") (license license:expat))) -(define-public rust-handlegraph-0.7 +(define-public rust-handlegraph-0.7.0-alpha.9 (package (name "rust-handlegraph") (version "0.7.0-alpha.9") @@ -180,7 +187,7 @@ functions} for a collection of hashable objects.") (define-public rust-handlegraph-0.3 (package - (inherit rust-handlegraph-0.7) + (inherit rust-handlegraph-0.7.0-alpha.9) (name "rust-handlegraph") (version "0.3.0") (source (origin @@ -221,6 +228,64 @@ functions} for a collection of hashable objects.") (description "Key String provides a Rust package optimized for map keys.") (license (list license:expat license:asl2.0)))) +(define-public rust-line-drawing-0.8 + (package + (name "rust-line-drawing") + (version "0.8.1") + (source (origin + (method url-fetch) + (uri (crate-uri "line-drawing" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "18a940s3mv8w5prpb99sdxykzhrvzrnymw3hvd7wisnkgbr11jqm")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-inputs + (("rust-num-traits" ,rust-num-traits-0.2)) + #:cargo-development-inputs + (("rust-bresenham" ,rust-bresenham-0.1) + ("rust-image" ,rust-image-0.23) + ("rust-rand" ,rust-rand-0.8)))) + (home-page "https://github.com/expenses/line_drawing") + (synopsis + "A collection of line-drawing algorithms for use in graphics and video games.") + (description + "This package provides a collection of line-drawing algorithms for use in +graphics and video games.") + (license license:expat))) + +(define-public rust-lodepng-3 + (package + (name "rust-lodepng") + (version "3.8.0") + (source (origin + (method url-fetch) + (uri (crate-uri "lodepng" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "1f5d9bva17sq7npw9qh7h6sh02k0ycrjx5hr147q0jv4m0qd2970")))) + (build-system cargo-build-system) + (arguments + `(#:cargo-test-flags + (list "--release" "--" + ;; Not all files included. + "--skip=test::read_icc") + #:cargo-inputs + (("rust-crc32fast" ,rust-crc32fast-1) + ("rust-fallible-collections" ,rust-fallible-collections-0.4) + ("rust-flate2" ,rust-flate2-1) + ("rust-libc" ,rust-libc-0.2) + ("rust-rgb" ,rust-rgb-0.8)))) + (home-page "https://lib.rs/crates/lodepng") + (synopsis + "Reading and writing PNG files without system dependencies. Pure Rust port of LodePNG.") + (description + "Reading and writing PNG files without system dependencies. Pure Rust port of +@code{LodePNG}.") + (license license:zlib))) + (define-public rust-pyo3-0.14 (package (name "rust-pyo3") @@ -475,76 +540,6 @@ or any combination.") (description "Rust CLI tools for manipulation of Jupyter Notebooks.") (license #f)))) ; There is no license. -(define-public rust-clap-4 - (package - (name "rust-clap") - (version "4.0.9") - (source (origin - (method url-fetch) - (uri (crate-uri "clap" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "1w0dxqzrh449s9l2k8g66pdsff02599bwi5mh0gny3227kcpsq1h")))) - (build-system cargo-build-system) - (arguments - `(#:skip-build? #t ; Not all inputs packaged. - #:cargo-inputs - (("rust-atty" ,rust-atty-0.2) - ("rust-backtrace" ,rust-backtrace-0.3) - ("rust-bitflags" ,rust-bitflags-1) - ("rust-clap-derive" ,rust-clap-derive-4) - ("rust-clap-lex" ,rust-clap-lex-0.3) - ("rust-once-cell" ,rust-once-cell-1) - ("rust-strsim" ,rust-strsim-0.10) - ("rust-termcolor" ,rust-termcolor-1) - ("rust-terminal-size" ,rust-terminal-size-0.1) - ("rust-unicase" ,rust-unicase-2) - ("rust-unicode-width" ,rust-unicode-width-0.1)) - ;#:cargo-development-inputs - ;(("rust-humantime" ,rust-humantime-2) - ; ("rust-rustversion" ,rust-rustversion-1) - ; ("rust-shlex" ,rust-shlex-1) - ; ("rust-snapbox" ,rust-snapbox-0.4) - ; ("rust-static-assertions" ,rust-static-assertions-1) - ; ("rust-trybuild" ,rust-trybuild-1) - ; ("rust-trycmd" ,rust-trycmd-0.13) - ; ("rust-unic-emoji-char" ,rust-unic-emoji-char-0.9)) - )) - (home-page "https://github.com/clap-rs/clap") - (synopsis - "A simple to use, efficient, and full-featured Command Line Argument Parser") - (description - "This package provides a simple to use, efficient, and full-featured Command Line - Argument Parser") - (license (list license:expat license:asl2.0)))) - -(define-public rust-clap-derive-4 - (package - (name "rust-clap-derive") - (version "4.0.9") - (source (origin - (method url-fetch) - (uri (crate-uri "clap-derive" version)) - (file-name (string-append name "-" version ".tar.gz")) - (sha256 - (base32 - "02zhbbmyz3dpy9ml6xfp7i8p3ffj1djvkdnkg6gr6d0s5r4hg8x4")))) - (build-system cargo-build-system) - (arguments - `(#:cargo-inputs - (("rust-heck" ,rust-heck-0.4) - ("rust-proc-macro-error" ,rust-proc-macro-error-1) - ("rust-proc-macro2" ,rust-proc-macro2-1) - ("rust-quote" ,rust-quote-1) - ("rust-syn" ,rust-syn-1)))) - (home-page "https://github.com/clap-rs/clap/tree/master/clap_derive") - (synopsis - "Parse command line argument by defining a struct, derive crate.") - (description - "Parse command line argument by defining a struct, derive crate.") - (license (list license:expat license:asl2.0)))) - (define-public rust-trycmd-0.12 (package (name "rust-trycmd") @@ -619,6 +614,32 @@ or any combination.") (description "Yet another format-preserving TOML parser.") (license (list license:expat license:asl2.0)))) +(define-public rust-vcf-0.6 + (package + (name "rust-vcf") + (version "0.6.1") + (source (origin + (method url-fetch) + (uri (crate-uri "vcf" version)) + (file-name (string-append name "-" version ".tar.gz")) + (sha256 + (base32 + "0dc0p00a19rpmhrqcshrn2qg5l716b5s1fy8vpd3p32bw77vpbs0")))) + (build-system cargo-build-system) + (arguments + `(#:tests? #f ; Not all files included + #:cargo-inputs + (("rust-nom" ,rust-nom-7) + ("rust-once-cell" ,rust-once-cell-1) + ("rust-thiserror" ,rust-thiserror-1)) + #:cargo-development-inputs + (("rust-clap" ,rust-clap-2) + ("rust-flate2" ,rust-flate2-1)))) + (home-page "https://github.com/informationsea/vcf-rs") + (synopsis "Rust implmentation of VCF parser") + (description "This package provides a rust implmentation of a VCF parser.") + (license license:asl2.0))) + (define-public rust-gsl-sys (package (name "rust-gsl-sys") diff --git a/gn/packages/cwl.scm b/gn/packages/cwl.scm index a327187..fe5fcb2 100644 --- a/gn/packages/cwl.scm +++ b/gn/packages/cwl.scm @@ -1,10 +1,19 @@ (define-module (gn packages cwl) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix download) + #:use-module (guix gexp) #:use-module (guix packages) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (gnu packages) - #:use-module (gnu packages bioinformatics)) + #:use-module (gnu packages bioinformatics) + #:use-module (gnu packages docker) + #:use-module (gnu packages node) + #:use-module (gnu packages python-web) + #:use-module (gnu packages python-xyz) + #:use-module (gnu packages serialization) + #:use-module (gnu packages time) + #:use-module (gn packages python)) (define-public cwl-runner @@ -28,3 +37,76 @@ "Common workflow language alternate entry point to allow cwl-runner script as an implementation-agnostic script interpreter.") (license license:asl2.0))) + +;; python-toil tightly integrates with cwltool using it as a library. So, +;; create a library version of cwltool where inputs become propagated inputs. +(define-public python-cwltool + (package + (inherit cwltool) + (name "python-cwltool") + (inputs + (list node)) + (propagated-inputs + (modify-inputs (package-inputs cwltool) + (delete "node"))))) + +(define-public python-toil + (package + (name "python-toil") + (version "6.1.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "toil" version)) + (sha256 + (base32 + "0hwaihnncsfxw0sf3iigvgw6nylrb56lpk8qjadkgazr98dsp4ha")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'disable-optional-features + (lambda _ + (substitute* "requirements-cwl.txt" + ;; Loosen version restrictions on ruamel.yaml. + (("ruamel.yaml[<>=.,[:digit:]]*\n") "ruamel.yaml\n") + ;; Remove optional dependency on galaxy-util and + ;; galaxy-tool-util. TODO: Package these and restore these + ;; dependencies. + (("galaxy-util[^\n]*") "") + (("galaxy-tool-util[^\n]*") "")) + ;; Disable optional wdl, wes and mesos features. We don't yet + ;; have dependencies packaged for them. TODO: Package these + ;; dependencies and enable these features. + (substitute* "setup.py" + (("\"wdl\",") "") + (("toil-cwl-runner = toil.cwl.cwltoil:main \\[cwl\\]") + "toil-cwl-runner = toil.cwl.cwltoil:main") + (("'toil-wdl-runner = toil.wdl.wdltoil:main \\[wdl\\]',") "") + (("'toil-wes-cwl-runner = toil.server.cli.wes_cwl_runner:main \\[server\\]',") "") + (("'_toil_mesos_executor = toil.batchSystems.mesos.executor:main \\[mesos\\]',") ""))))))) + (propagated-inputs + (list python-addict + python-cachecontrol + python-configargparse + python-cwltool + python-dateutil + python-dill + python-docker + python-enlighten + python-psutil + python-pypubsub + python-pytz + python-pyyaml + python-requests + python-ruamel.yaml + python-typing-extensions-4.10 + python-urllib3)) + (home-page "https://github.com/DataBiosphere/toil") + (synopsis "Scalable, efficient and cross-platform workflow engine") + (description "Toil is a scalable, efficient, cross-platform pipeline +management system, written entirely in Python, and designed around the +principles of functional programming.") + (license (list license:asl2.0 ;; main license + license:expat)))) ;; src/toil/batchSystems/lsf.py and + ;; src/toil/batchSystems/lsfHelper.py diff --git a/gn/packages/datastructures.scm b/gn/packages/datastructures.scm new file mode 100644 index 0000000..1744420 --- /dev/null +++ b/gn/packages/datastructures.scm @@ -0,0 +1,117 @@ +;; Datastructures module + +(define-module (gn packages datastructures) + #:use-module (guix packages) + #:use-module (guix gexp) + #:use-module (guix utils) + #:use-module (gnu packages datastructures)) + +(define sdsl-lite-x86-64-v2 + (package/inherit sdsl-lite + (name "sdsl-lite-x86-64-v2") + (arguments + (substitute-keyword-arguments (package-arguments sdsl-lite) + ((#:configure-flags flags #~'()) + #~(append (list "-DCMAKE_CXX_FLAGS=-march=x86-64-v2" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v2" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v2")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/include")))) + (replace 'install-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v2/libsdsl.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (copy-file "lib/libsdsl_static.a" + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +(define sdsl-lite-x86-64-v3 + (package/inherit sdsl-lite + (name "sdsl-lite-x86-64-v3") + (arguments + (substitute-keyword-arguments (package-arguments sdsl-lite) + ((#:configure-flags flags #~'()) + #~(append (list "-DCMAKE_CXX_FLAGS=-march=x86-64-v3" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v3" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v3")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/include")))) + (replace 'install-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v3/libsdsl.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (copy-file "lib/libsdsl_static.a" + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +(define sdsl-lite-x86-64-v4 + (package/inherit sdsl-lite + (name "sdsl-lite-x86-64-v4") + (arguments + (substitute-keyword-arguments (package-arguments sdsl-lite) + ((#:configure-flags flags #~'()) + #~(append (list "-DCMAKE_CXX_FLAGS=-march=x86-64-v4" + "-DCMAKE_INSTALL_LIBDIR=lib/glibc-hwcaps/x86-64-v4" + (string-append "-DCMAKE_INSTALL_RPATH=" #$output + "/lib/glibc-hwcaps/x86-64-v4")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/include")))) + (replace 'install-static-library + (lambda* (#:key outputs #:allow-other-keys) + (let ((lib "/lib/glibc-hwcaps/x86-64-v4/libsdsl.a")) + (mkdir-p (dirname (string-append #$output:static lib))) + (copy-file "lib/libsdsl_static.a" + (string-append #$output:static lib))))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t))))) + +(define-public sdsl-lite-hwcaps + (package/inherit sdsl-lite + (name "sdsl-lite-hwcaps") + (arguments + (substitute-keyword-arguments (package-arguments sdsl-lite) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'install-optimized-libraries + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((hwcaps "/lib/glibc-hwcaps")) + (copy-recursively + (string-append (assoc-ref inputs "sdsl-lite-x86-64-v2") + hwcaps "/x86-64-v2") + (string-append #$output hwcaps "/x86-64-v2")) + (copy-recursively + (string-append (assoc-ref inputs "sdsl-lite-x86-64-v3") + hwcaps "/x86-64-v3") + (string-append #$output hwcaps "/x86-64-v3")) + (copy-recursively + (string-append (assoc-ref inputs "sdsl-lite-x86-64-v4") + hwcaps "/x86-64-v4") + (string-append #$output hwcaps "/x86-64-v4"))))))))) + (native-inputs + (modify-inputs (package-native-inputs sdsl-lite) + (append sdsl-lite-x86-64-v2 + sdsl-lite-x86-64-v3 + sdsl-lite-x86-64-v4))) + (properties `((tunable? . #f))))) diff --git a/gn/packages/file-systems.scm b/gn/packages/file-systems.scm index 709754a..bf92ed9 100644 --- a/gn/packages/file-systems.scm +++ b/gn/packages/file-systems.scm @@ -28,7 +28,8 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0zk73wmx82ari3m2mv0zx04x1ggsdmwcwn7k6bkl5c0jnxffc4ax")))) + "0zk73wmx82ari3m2mv0zx04x1ggsdmwcwn7k6bkl5c0jnxffc4ax")) + (patches (search-patches "lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch")))) (build-system cmake-build-system) (arguments `(#:configure-flags @@ -58,8 +59,7 @@ (("etc/mfs") "/etc/lizardfs")) ;; Then adjust the install instructions. (substitute* "src/data/CMakeLists.txt" - (("^install.*") "")) - #t)) + (("^install.*") "")))) (add-after 'unpack 'use-system-libraries (lambda* (#:key inputs #:allow-other-keys) (let ((gtest (assoc-ref inputs "googletest")) @@ -99,9 +99,7 @@ ;; fix FTBFS with glibc-2.28; for makedev ;; https://github.com/lizardfs/lizardfs/issues/655 (substitute* "src/chunkserver/iostat.h" - (("sys/stat.h>") "sys/stat.h>\n#include <sys/sysmacros.h>")) - - #t))) + (("sys/stat.h>") "sys/stat.h>\n#include <sys/sysmacros.h>"))))) (add-after 'install 'install-extras ;; This got broken by changing the directories above. (lambda* (#:key outputs #:allow-other-keys) @@ -120,16 +118,15 @@ (lambda (file) (copy-file file (string-append etc "/" (basename file) ".dist"))) - (find-files data "\\.cfg(\\.in)?$")) - #t))))))) + (find-files data "\\.cfg(\\.in)?$"))))))))) (inputs - `(("bdb" ,bdb) - ("boost" ,boost) - ("fuse" ,fuse) - ("linux-pam" ,linux-pam) - ("python" ,python-2) - ("spdlog" ,spdlog) - ("zlib" ,zlib))) + (list bdb + boost + fuse-2 + linux-pam + python-2 + spdlog + zlib)) (native-inputs `(("asciidoc" ,asciidoc) ("googletest" ,(package-source googletest-1.7)) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 36d3ae6..10619da 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -5,6 +5,7 @@ #:use-module (guix packages) #:use-module (guix utils) #:use-module (guix download) + #:use-module (guix git) #:use-module (guix git-download) #:use-module (guix build-system cargo) #:use-module (guix build-system gnu) @@ -14,6 +15,7 @@ #:use-module (guix scripts graph) #:use-module (guix store) #:use-module (guix gexp) + #:use-module (guix packages) #:use-module (gnu packages) #:use-module (gnu packages base) #:use-module (gnu packages bioconductor) @@ -110,10 +112,11 @@ ((#:tests? _ #f) #f))))) (define-public genenetwork3 - (let ((commit "f52247c15f3694f3dd5fd0fd79c3e15376137e07")) + (let ((commit "6bb4a5f05c1a2c96b7da1780ae4a1d70c7cc4afb") + (revision "5")) (package (name "genenetwork3") - (version (git-version "0.1.0" "3" commit)) + (version (git-version "0.1.0" revision commit)) (source (origin (method git-fetch) @@ -123,52 +126,51 @@ (file-name (git-file-name name version)) (sha256 (base32 - "0ac0dr8dny65x4xvm8gw6ap3g8g0j933ipy9116idcws31rk2adk")))) + "13nvi2gwwb0shra0d9rsfhppa9ky4bhgh1zgb34790ax0g9lwa97")))) (inputs (list python-click)) (native-inputs (list python-hypothesis python-mypy python-mypy-extensions - python-pylint - python-pytest - python-pytest-mock)) + python-pylint)) (propagated-inputs - (list gemma-wrapper - python-wrapper - csvdiff + (list csvdiff + diffutils + gemma-wrapper gn-rust-correlation - python-bcrypt ;; Replace use of bcrypt with argon below - python-argon2-cffi + python-argon2-cffi + python-authlib + python-bcrypt ;; Replace use of bcrypt with argon + python-biopython + python-email-validator python-flask python-flask-cors - ;; Not working in Python > 3.8 - ;; python-ipfshttpclient python-lmdb python-mysqlclient python-numpy python-pandas - ;; python-pingouin << build failing python-pingouin-without-tests python-plotly - python-scikit-learn + python-pyld python-pymonad + python-pytest + python-pytest-mock python-redis python-requests + python-scikit-learn python-scipy - python-authlib python-sparqlwrapper - python-email-validator + python-wrapper python-xapian-bindings + r + r-ctl r-optparse r-qtl r-rjson r-stringi r-wgcna - r-ctl - rust-qtlreaper - diffutils - yoyo-migrations)) + rust-qtlreaper)) (build-system python-build-system) (arguments (list #:phases @@ -183,10 +185,11 @@ (license license:agpl3+)))) (define-public genenetwork2 - (let ((commit "bfe557dc1e537dc78a82a30817ecf2ca3004d978")) + (let ((commit "b9e04ad79e0039edba25d58f8bc03e4d2a17583b") + (revision "4")) (package (name "genenetwork2") - (version (git-version "3.11" "2" commit)) + (version (git-version "3.11" revision commit)) (source (origin (method git-fetch) (uri (git-reference @@ -195,273 +198,318 @@ (file-name (string-append name "-" version)) (sha256 (base32 - "1bn0j0fpk4hcicgfird62x5wq2n6lj4rs1ggw69dcxyf4qdxbk5d")))) + "1ri56g5hl2n0q7cz15sbvjmrr5pmsrp274frkvvcgr9ddxjlzd9p")))) (native-inputs (list graphviz)) (propagated-inputs - `(("genenetwork3" ,genenetwork3) - ("parallel" ,parallel) ;; GNU parallel - ("coreutils" ,coreutils) - ("git" ,git) - ("which" ,which) - ("grep" ,grep) - ("r" ,r) - ("r-ctl" ,r-ctl) - ("r-qtl" ,r-qtl) - ("r-wgcna" ,r-wgcna) - ("redis" ,redis) - ("mariadb" ,mariadb) - ("gemma" ,gemma-gn2) - ("gemma-wrapper" ,gemma-wrapper) - ("plink-ng-gn" ,plink-ng-gn) - ("rust-qtlreaper" ,rust-qtlreaper) - ("gn-rust-correlation" ,gn-rust-correlation) - ("glibc-utf8-locales" ,glibc-utf8-locales) - ("nginx" ,nginx) - ("python" ,python-wrapper) - ("python-pillow" ,python-pillow) - ("python-coverage" ,python-coverage) - ("python-configparser" ,python-configparser) ;; maintenance/scripts - ("python-flask" ,python-flask) - ("gunicorn" ,gunicorn) - ("python-autopep8" ,python-autopep8) - ("python-cssselect" ,python-cssselect) - ("python-flask-debugtoolbar" ,python-flask-debugtoolbar) - ("python-htmlgen" ,python-htmlgen) - ("python-ijson" ,python-ijson) - ("python-jinja2" ,python-jinja2) - ("python-pytest" ,python-pytest) - ("python-pytest-mock" ,python-pytest-mock) - ("python-sqlalchemy" ,python-sqlalchemy) - ("python-setuptools" ,python-setuptools) - ("python-scipy" ,python-scipy) - ("python-lxml" ,python-lxml) - ("python-mysqlclient" ,python-mysqlclient) - ("python-mypy" ,python-mypy) - ("python-numpy" ,python-numpy) - ("python-pandas" ,python-pandas) - ("python-pylint" ,python-pylint) - ("python-pymonad" ,python-pymonad) - ("python-redis" ,python-redis) - ("python-requests" ,python-requests) - ("python-simplejson" ,python-simplejson) - ("python-markdown" ,python-markdown) - ("python-rdflib" ,python-rdflib) - ("python-authlib" ,python-authlib) - ("python-flask-session" ,python-flask-session) - ;; TODO: Get rid of Python R bindings - ("python-rpy2" ,python-rpy2) - ("python-beautifulsoup4" ,python-beautifulsoup4) - ;; Disable for now. Build fails on Penguin2 - ;; ("python-flask-socketio" ,python-flask-socketio) - ("python-xlsxwriter" ,python-xlsxwriter) - ;; All the external js dependencies - ("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher) - ("javascript-cytoscape" ,javascript-cytoscape) - ("javascript-panzoom" ,javascript-cytoscape-panzoom) - ("javascript-qtip" ,javascript-cytoscape-qtip) - ("javascript-chroma" ,javascript-chroma) - ("javascript-d3-tip" ,javascript-d3-tip) - ("javascript-jscolor" ,javascript-jscolor) - ("javascript-colorbox" ,javascript-colorbox) - ("javascript-jszip" ,javascript-jszip) - ("js-jstat" ,js-jstat) - ("js-md5" ,js-md5) - ("js-parsley" ,js-parsley) - ("javascript-plotly" ,javascript-plotly) - ("javascript-typeahead" ,javascript-typeahead) - ("js-underscore" ,js-underscore) - ("js-smart-time-ago" ,js-smart-time-ago) - ("javascript-nouislider" ,javascript-nouislider) - ("javascript-purescript-genome-browser" ,javascript-purescript-genome-browser) - ("javascript-ckeditor" ,javascript-ckeditor) - ("javascript-datatables" ,javascript-datatables) - ("javascript-datatables-scroller" ,javascript-datatables-scroller) - ("javascript-datatables-buttons" ,javascript-datatables-buttons) - ("javascript-datatables-buttons-bootstrap" ,javascript-datatables-buttons-bootstrap) - ("javascript-datatables-plugins" ,javascript-datatables-plugins) - ("javascript-datatables-col-reorder" ,javascript-datatables-col-reorder) - ("javascript-datatables-col-resize" ,javascript-datatables-col-resize) - ("javascript-datatables-buttons-styles" ,javascript-datatables-buttons-styles) - ("javascript-shapiro-wilk" ,javascript-shapiro-wilk) - ("javascript-underscore-string" ,javascript-underscore-string) - ("javascript-qtip2" ,javascript-qtip2) - ("javascript-d3js" ,javascript-d3js) - ("javascript-nvd3" ,javascript-nvd3) - ("javascript-bootstrap" ,javascript-bootstrap) - ("javascript-jquery" ,javascript-jquery) - ("javascript-zxcvbn" ,javascript-zxcvbn) - ("javascript-jquery-ui" ,javascript-jquery-ui) - ("javascript-jquery-cookie" ,javascript-jquery-cookie) - ("javascript-xterm" ,javascript-xterm) - ("javascript-xterm-style" ,javascript-xterm-style) - ("javascript-xterm-addon-fit",javascript-xterm-addon-fit) - ("javascript-font-awesome" ,javascript-font-awesome))) + (list genenetwork3 + coreutils + gemma + gemma-wrapper + git + glibc-utf8-locales + gn-rust-correlation + grep + gunicorn + javascript-bootstrap + javascript-chroma + javascript-ckeditor + javascript-colorbox + javascript-cytoscape + javascript-cytoscape-panzoom + javascript-cytoscape-qtip + javascript-d3-tip + javascript-d3js ;; very old + javascript-d3js-7 + javascript-d3panels + javascript-datatables + javascript-datatables-buttons + javascript-datatables-buttons-bootstrap + javascript-datatables-buttons-styles + javascript-datatables-col-reorder + javascript-datatables-col-resize + javascript-datatables-plugins + javascript-datatables-scroller + javascript-font-awesome + javascript-htmx + javascript-jquery + javascript-jquery-cookie + javascript-jquery-ui + javascript-jscolor + javascript-jszip + javascript-linkify + javascript-linkify-html + javascript-nouislider + javascript-nvd3 + javascript-plotly + javascript-purescript-genome-browser + javascript-qtip2 + javascript-shapiro-wilk + javascript-twitter-post-fetcher + javascript-typeahead + javascript-uikit + javascript-underscore-string + javascript-zxcvbn + js-jstat + js-md5 + js-parsley + js-smart-time-ago + js-underscore + mariadb + nginx + parallel + plink-ng-gn + python-authlib + python-autopep8 + python-beautifulsoup4 + python-configparser + python-coverage + python-cssselect + python-flask + python-flask-debugtoolbar + python-flask-session + python-htmlgen + python-ijson + python-jinja2 + python-lxml + python-markdown + python-mypy + python-mysqlclient + python-numpy + python-pandas + python-pillow + python-pylint + python-pymonad + python-pytest + python-pytest-mock + python-rdflib + python-redis + python-requests + python-rpy2 + python-scipy + python-setuptools + python-simplejson + python-sqlalchemy + python-wrapper + python-xlsxwriter + r + r-ctl + r-qtl + r-wgcna + redis + rust-qtlreaper + which + ; javascript-xterm -- disabled until we know what to do with it, not working on production + ; javascript-xterm-style + ; javascript-xterm-addon-fit + )) (inputs - `(("javascript-colorbox" ,(package-source javascript-colorbox)))) + (list javascript-colorbox)) (build-system python-build-system) (arguments - `(#:tests? #f ; no 'setup.py test' + (list #:tests? #f + #:phases + #~(modify-phases %standard-phases + (delete 'reset-gzip-timestamps) + (add-after 'unpack 'fix-paths-to-static-files + (lambda* (#:key inputs outputs #:allow-other-keys) + ;; Set absolute store paths to installed static files. + (substitute* "gn2/wqflask/marker_regression/display_mapping_results.py" + (("\\./gn2/wqflask/static/fonts") + (string-append (site-packages inputs outputs) + "/gn2/wqflask/static/fonts"))) + (substitute* "gn2/wqflask/views.py" + (("\\./gn2/wqflask/static/gif/error") + (string-append (site-packages inputs outputs) + "/gn2/wqflask/static/gif/error"))) + (substitute* "gn2/wqflask/app_errors.py" + (("\\./gn2/wqflask/static/gif/error") + (string-append (site-packages inputs outputs) + "/gn2/wqflask/static/gif/error"))))) + (add-after 'unpack 'fix-paths-scripts + (lambda _ + (substitute* "bin/genenetwork2" + (("/usr/bin/env") (which "env")) + (("python ") (string-append (which "python3") " ")) + (("readlink") (which "readlink")) + (("dirname") (which "dirname")) + (("basename") (which "basename")) + (("cat") (which "cat")) + (("echo") (which "echo")) + (("redis-server") (which "redis-server")) + (("git") (which "git")) + (("grep") (which "grep")) + (("rm") (which "rm")) + (("which") (which "which"))))) + (add-before 'install 'fix-paths + (lambda* (#:key inputs #:allow-other-keys) + (let* ((plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) + (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))) + (substitute* '("gn2/default_settings.py") + (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) + (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" ))))))))) + (home-page "http://genenetwork.org/") + (synopsis "Full genenetwork services") + (description "Genenetwork installation sumo.") + (license license:agpl3+)))) + +(define-public genenetwork3-stable + (let ((commit "e5569c3bb1c0d59ff7142273c5f51fe19f06cfe8") + (revision "1")) + (package + (inherit genenetwork3) + (name "genenetwork3-stable") + (version (string-append (git-version "3.11" revision commit))) + (arguments + (list + #:tests? #f #:phases - (modify-phases %standard-phases - (delete 'reset-gzip-timestamps) - (add-after 'unpack 'fix-paths-scripts - (lambda _ - (substitute* "bin/genenetwork2" - (("/usr/bin/env") (which "env")) - (("python ") (string-append (which "python3") " ")) - (("readlink") (which "readlink")) - (("dirname") (which "dirname")) - (("basename") (which "basename")) - (("cat") (which "cat")) - (("echo") (which "echo")) - (("redis-server") (which "redis-server")) - (("git") (which "git")) - (("grep") (which "grep")) - (("rm") (which "rm")) - (("which") (which "which"))) - #t)) - ; (add-after 'unpack 'patch-javascript - ; (lambda* (#:key inputs #:allow-other-keys) - ; (let ((colorbox (assoc-ref inputs "javascript-colorbox")) - ; (gn2 "/share/genenetwork2/javascript/")) - ; (delete-file-recursively "wqflask/wqflask/static/packages/colorbox") - ; (copy-recursively colorbox "wqflask/wqflask/static/packages/colorbox") - ; #t))) - (add-before 'install 'fix-paths - (lambda* (#:key inputs #:allow-other-keys) - (let* ( - ; (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2")) - ; (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) - (plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) - (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) - ) + #~(modify-phases %standard-phases + (add-before 'build 'update-paths + (lambda _ + (for-each (lambda (fn) + (substitute* (string-append "gn3/" fn) + (("scripts/") + (string-append #$output "/scripts/")))) + '("api/rqtl.py" + "computations/wgcna.py" + "computations/ctl.py" + "api/general.py")))) + (add-before 'install 'install-scripts + (lambda _ + (begin + (mkdir (string-append #$output "scripts")) + (for-each (lambda (fn) + (install-file fn + (string-append #$output "/scripts"))) + '("scripts/rqtl_wrapper.R" + "scripts/ctl_analysis.R" + "scripts/wgcna_analysis.R" + )))))))) - (substitute* '("etc/default_settings.py") - ; (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) - ; (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) - (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) - (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) - ) - ))) - ; (add-after 'install 'generate-graph - ; (lambda* (#:key inputs outputs #:allow-other-keys) - ; (call-with-output-file - ; (string-append - ; (assoc-ref outputs "out") - ; "/lib/python" - ; (python-version (assoc-ref inputs "python")) - ; "/site-packages" - ; "/wqflask/dependency-graph.html") - ; (lambda (port) - ; (format - ; port "~a" - ; ,(call-with-output-string - ; (lambda (p) - ; (with-output-to-port p - ; (lambda () - ; (run-with-store - ; (open-connection) - ; (export-graph - ; (list this-package) - ; p - ; #:node-type %package-node-type - ; #:backend %d3js-backend))))))))))) - ;(add-after 'install 'generate-dag-svg-file - ; (lambda* (#:key inputs outputs #:allow-other-keys) - ; (let* ((output-dir - ; (string-append - ; (assoc-ref outputs "out") - ; "/lib/python" - ; (python-version (assoc-ref inputs "python")) - ; "/site-packages/wqflask/")) - ; (dot-file - ; (string-append - ; output-dir - ; "dependency-graph.dot")) - ; (svg-file - ; (string-append - ; output-dir - ; "dependency-graph.svg"))) - ; (begin - ; (call-with-output-file - ; dot-file - ; (lambda (port) - ; (format - ; port "~a" - ; ,(call-with-output-string - ; (lambda (p) - ; (with-output-to-port p - ; (lambda () - ; (run-with-store - ; (open-connection) - ; (export-graph - ; (list this-package) - ; p - ; #:node-type %package-node-type - ; #:backend %graphviz-backend))))))))) - ; (invoke "dot" "-Tsvg" "-o" svg-file dot-file))))) + (source + (git-checkout + (url "https://github.com/genenetwork/genenetwork3") + (branch "prod")))))) - ;; TODO: Use this to replace the two previous phases. - ;(add-after 'install 'install-generated-files - ; (lambda* (#:key inputs outputs #:allow-other-keys) - ; (let ((output-dir - ; (string-append - ; (assoc-ref outputs "out") - ; "/lib/python" - ; (python-version (assoc-ref inputs "python")) - ; "/site-packages/wqflask/"))) - ; (install-file (string-append %dag-svg-file "/dependency-graph.dot") output-dir) - ; (install-file (string-append %dag-svg-file "/dependency-graph.svg") output-dir) - ; (install-file (string-append %genenetwork-graph "/dependency-graph.html") output-dir) - ; #t))) +(define-public genenetwork2-stable + (let ((commit "95e634ca90d52922812b93df162686b348288651") + (revision "1")) + (package + (inherit genenetwork2) + (name "genenetwork2-stable") + (version (string-append "stable-" (git-version "3.12" revision commit))) + (source + (git-checkout + (url "https://github.com/genenetwork/genenetwork2") + (branch "prod"))) + (arguments + (list + #:tests? #f + #:phases + #~(modify-phases %standard-phases + (add-before 'build 'update-font-paths + (lambda* (#:key inputs outputs #:allow-other-keys) + (for-each (lambda (fn) + (substitute* (string-append "gn2/" fn) + (("\\./gn2/wqflask/static/fonts/") + (string-append (site-packages inputs outputs) "/gn2/wqflask/static/fonts/")))) + '("utility/Plot.py" + "wqflask/marker_regression/display_mapping_results.py")))) + )))))) - #! - (add-after 'install 'generate-dependency-file - (lambda* (#:key inputs outputs #:allow-other-keys) - (call-with-output-file - (string-append - (assoc-ref outputs "out") - "/lib/python" - (python-version (assoc-ref inputs "python")) - "/site-packages" - "/wqflask/DEPENDENCIES.md" - ) - (lambda (port) - (format - port " -#### System Inputs (generated from ~a package defined in ~a) -|Name | Description | -|-----|-------------| -~a -" - ,(package-name this-package) - (string-append - "[genenetwork.scm]" - "(http://git.genenetwork.org/" - "guix-bioinformatics/guix-bioinformatics" - "/src/branch/master/gn/packages/" - "genenetwork.scm)") - ,(apply - string-append - (map - (lambda (input) - (let* ((pkg (cadr input)) - (name (package-name pkg)) - (version (package-version pkg)) - (home-page (package-home-page pkg)) - (description (package-synopsis pkg))) - (string-append - "| **[" name "](" home-page ")** v" - version"| " - description " |\n"))) - (package-propagated-inputs this-package)))))))) - !# - ))) - (home-page "http://genenetwork.org/") - (synopsis "Full genenetwork services") - (description "Genenetwork installation sumo.") - (license license:agpl3+)))) +(define-public gn-uploader + (let ((commit "60fde66e02dba842b20fa126ff3b2ed9ec2638e6") + (version "0.0.1")) + (package + (name "gn-uploader") + (version (string-append version "-" (string-take commit 8))) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://git.genenetwork.org/gn-uploader") + (commit commit))) + (hash + (content-hash + (base32 + "1q04viyf7d0q30k3424hrzsh9wxhhgs7hywlhzl3m68jki4zq1i7"))))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-m" "unit_test"))))))) + (native-inputs + (list python-mypy + python-pylint + python-pytest + python-hypothesis)) + (propagated-inputs + (list gunicorn + python-redis + python-flask + python-pyyaml + python-jsonpickle + python-mysqlclient + javascript-jquery + javascript-bootstrap)) + (synopsis "GeneNetwork Quality Control Application") + (description + "gn-uploader is a service allowing upload of new data into GeneNetwork, + that does quality control for the data files that is being uploaded to ensure + it fulfils all conditions before it can be accepted.") + (home-page "https://git.genenetwork.org/gn-uploader") + (license license:agpl3+)))) + +(define-public gn-auth + (package + (name "gn-auth") + (version "1.0.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/genenetwork/gn-auth.git") + (commit "cd6eebd85d32feb289ccecd1aee45fb40b03d77f"))) + (hash + (content-hash + (base32 + "06slj3z110mbc46qncdvyi29y85zkqxl76n89dxjp5wjfqxw0nsl"))))) + (build-system python-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-k" "unit_test"))))))) + (native-inputs + (list python-hypothesis + python-mypy + python-mypy-extensions + python-pylint + python-pytest + python-pytest-mock)) + (propagated-inputs + (list gunicorn + python-argon2-cffi + python-authlib + python-email-validator + python-flask + python-flask-cors + python-mysqlclient + python-pymonad + python-redis + yoyo-migrations)) + (home-page "https://github.com/genenetwork/gn-auth") + (synopsis "Authentication and Authorisation server for GeneNetwork services") + (description "Authentication and Authorisation server for GeneNetwork services.") + (license license:agpl3+))) ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x @@ -469,41 +517,41 @@ (define-public genenetwork2-files-small (let ((pfff "xx")) (package - (name "genenetwork2-files-small") - (version "1.0") - (source - (origin - (method url-fetch) - (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4") - (file-name (string-append name "-" pfff)) - (sha256 - (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj")))) - (build-system trivial-build-system) - (native-inputs `(("lz4" ,lz4) - ("tar" ,tar) - ("source" ,source))) + (name "genenetwork2-files-small") + (version "1.0") + (source + (origin + (method url-fetch) + (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4") + (file-name (string-append name "-" pfff)) + (sha256 + (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj")))) + (build-system trivial-build-system) + (native-inputs `(("lz4" ,lz4) + ("tar" ,tar) + ("source" ,source))) - (arguments - `(#:modules ((guix build utils)) - #:builder - (let* ((out (assoc-ref %outputs "out")) - (name "gn2_data_s") - (tarfn (string-append name ".tar")) - (targetdir (string-append out "/share/genenetwork2/"))) + (arguments + `(#:modules ((guix build utils)) + #:builder + (let* ((out (assoc-ref %outputs "out")) + (name "gn2_data_s") + (tarfn (string-append name ".tar")) + (targetdir (string-append out "/share/genenetwork2/"))) (begin (use-modules (guix build utils)) (let ((source (assoc-ref %build-inputs "source")) (lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4")) (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar"))) (and - (zero? (system* lz4unpack source "-d" tarfn)) - (zero? (system* tar "xf" tarfn)) - (mkdir-p targetdir) - (copy-recursively name targetdir))))))) - (home-page "http://genenetwork.org/") - (synopsis "Small file archive to run on genenetwork") - (description "Genenetwork genotype and mapping files.") - (license license:agpl3+)))) + (zero? (system* lz4unpack source "-d" tarfn)) + (zero? (system* tar "xf" tarfn)) + (mkdir-p targetdir) + (copy-recursively name targetdir))))))) + (home-page "http://genenetwork.org/") + (synopsis "Small file archive to run on genenetwork") + (description "Genenetwork genotype and mapping files.") + (license license:agpl3+)))) (define-public genenetwork2-database-small (let ((md5 "93e745e9c")) diff --git a/gn/packages/globus.scm b/gn/packages/globus.scm new file mode 100644 index 0000000..6cc5d9e --- /dev/null +++ b/gn/packages/globus.scm @@ -0,0 +1,76 @@ +(define-module (gn packages globus) + #:use-module (gnu packages check) + #:use-module (gnu packages python-build) + #:use-module (gnu packages python-crypto) + #:use-module (gnu packages python-web) + #:use-module (gnu packages python-xyz) + #:use-module (guix build-system pyproject) + #:use-module (guix build-system python) + #:use-module (guix download) + #:use-module ((guix licenses) #:prefix license:) + #:use-module (guix packages)) + +(define-public python-globus-sdk + (package + (name "python-globus-sdk") + (version "3.37.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "globus-sdk" version)) + (sha256 + (base32 + "19w3pjzfycaqvvr11nq8c91i6pkkkic95yf170hr39dwj70lrkc7")))) + (build-system pyproject-build-system) + (propagated-inputs (list python-cryptography python-pyjwt python-requests + python-typing-extensions)) + (home-page "https://github.com/globus/globus-sdk-python") + (synopsis "Globus SDK for Python") + (description "@code{python-globus-sdk} provides a convenient Pythonic interface to +Globus APIs.") + (license license:asl2.0))) + +(define-public python-click-type-test + (package + (name "python-click-type-test") + (version "0.0.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "click-type-test" version)) + (sha256 + (base32 + "1i3z7akiz7s8jy6x0vzrak88m55ac1spq88vziwryzr7355y3hgq")))) + (build-system pyproject-build-system) + (native-inputs (list python-pytest)) + (propagated-inputs (list python-click)) + (home-page "https://github.com/sirosen/click-type-test") + (synopsis "Test that type annotations match click parameter types") + (description "@code{python-click-type-test} allows you to test that your click +options and arguments match your type annotations.") + (license license:expat))) + +(define-public globus-cli + (package + (name "globus-cli") + (version "3.25.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "globus-cli" version)) + (sha256 + (base32 + "05div2psajmqdy9md804q4x6ha4yfp4w6yrxz0ynsq3i62a6cl5v")))) + (build-system pyproject-build-system) + (arguments + (list #:tests? #f)) + (propagated-inputs + (list python-click + python-cryptography + python-globus-sdk + python-jmespath + python-packaging + python-requests + python-typing-extensions)) + (home-page "https://docs.globus.org/cli") + (synopsis "Globus CLI") + (description "@code{globus-cli} provides a command-line interface to +Globus APIs.") + (license license:asl2.0))) diff --git a/gn/packages/java.scm b/gn/packages/java.scm index cdd9d00..f39c5c7 100644 --- a/gn/packages/java.scm +++ b/gn/packages/java.scm @@ -19,6 +19,7 @@ (define-module (gn packages java) #:use-module ((guix licenses) #:prefix license:) #:use-module (guix packages) + #:use-module (guix gexp) #:use-module (guix utils) #:use-module (guix download) #:use-module (guix git-download) @@ -27,16 +28,24 @@ #:use-module (guix build-system ant) #:use-module (gnu packages) #:use-module (gnu packages autotools) + #:use-module (gnu packages bash) #:use-module (gnu packages bioinformatics) #:use-module (gnu packages certs) #:use-module (gnu packages compression) + #:use-module (gnu packages cups) #:use-module (gnu packages gcc) - #:use-module (gnu packages icu4c) #:use-module (gnu packages java) #:use-module (gnu packages java-compression) #:use-module (gnu packages perl) #:use-module (srfi srfi-1)) +;; This is an attempt to make a smaller version of openjdk +(define openjdk11-minimal + (package/inherit openjdk11 + (inputs + (modify-inputs (package-inputs openjdk11) + (replace "cups" cups-minimal))))) + ;; ---------------------------------------------------------------------------- ;; WORKING PACKAGES ;; ---------------------------------------------------------------------------- @@ -315,7 +324,8 @@ piece of information.") (base32 "13fjhhcjgnynxscaymkn3rpdciplbg2m2qmihc7fxsylgn4m6gxk")))) (build-system ant-build-system) (arguments - `(#:build-target "zip-nojre" + `(#:jdk ,openjdk11-minimal + #:build-target "zip-nojre" #:test-target "runalltests" #:phases (modify-phases %standard-phases @@ -325,8 +335,7 @@ piece of information.") (("\"git\"") "\"echo\"") (("\\$\\{vcs\\.cmd\\.out\\}") "${product.version}") (("\\$\\{build\\.time\\}") "1970-01-01") - (("-\\$\\{rtg\\.vcs\\.commit\\.revision\\}") "")) - #t)) + (("-\\$\\{rtg\\.vcs\\.commit\\.revision\\}") "")))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out")) @@ -337,52 +346,59 @@ piece of information.") (invoke "unzip" (string-append pkg "-nojre.zip")) (copy-recursively (string-append pkg "/") ".") (delete-file-recursively pkg) - (delete-file (string-append pkg "-nojre.zip"))) - #t))) + (delete-file (string-append pkg "-nojre.zip")))))) (add-after 'install 'create-rtg.cfg - (lambda* (#:key outputs #:allow-other-keys) + (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) (with-output-to-file (string-append out "/rtg.cfg") (lambda _ (format #t "RTG_JAVA=\"~a\"~@ RTG_TALKBACK=false~@ RTG_USAGE=false~%" - (which "java")))) - #t))) - (add-after 'install 'install-completions - (lambda* (#:key outputs #:allow-other-keys) - (install-file "installer/resources/common/scripts/rtg-bash-completion" - (string-append (assoc-ref outputs "out") - "/share/bash-completion/completions")) - #t)) + (search-input-file inputs "/bin/java"))))))) + (add-after 'install 'create-wrapper-script + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (wrapper (string-append out "/bin/rtg"))) + ;; We want an executable in the bin directory without rewriting + ;; the existing wrapper script. + (mkdir-p (dirname wrapper)) + (with-output-to-file wrapper + (lambda _ + (format #t "#!~a~@ + exec -a \"$0\" \"~a/rtg\" \"$@\"~%" + (search-input-file inputs "/bin/bash") + out))) + (chmod wrapper #o555)))) + (add-after 'install 'install-completions + (lambda* (#:key outputs #:allow-other-keys) + (install-file "installer/resources/common/scripts/rtg-bash-completion" + (string-append (assoc-ref outputs "out") + "/share/bash-completion/completions")))) (delete 'generate-jar-indices)))) ; manually installed (inputs - `(("java-commons-collections" ,java-commons-collections) - ("java-commons-compress" ,java-commons-compress) - ("java-commons-lang" ,java-commons-lang) - ;("java-graal-sdk" ,java-graal-sdk) - ;("java-gzipfix" ,java-gzipfix) - ;("java-htsjdk" ,java-sam-rtg) - ("java-icu4j" ,java-icu4j) - ;("java-js" ,java-js) - ;("java-js-scriptengine" ,java-js-scriptengine) - ;("java-json-simple" ,java-json-simple) - ;("java-regex" ,java-regex) - ;("java-rplot" ,java-rplot) - ("java-snappy" ,java-snappy) - ;("java-truffle-api" ,java-truffle-api) - ;("java-velocity" ,java-velocity) - ;("java-velocity-tools-generic" ,java-velocity-tools-generic) - )) + (list bash-minimal ; for the wrapper script + java-commons-collections + java-commons-compress + java-commons-lang + ;java-gzipfix + ;java-sam-rtg + ;java-json-simple + ;java-rplot + java-snappy + ;java-velocity + ;java-velocity-tools-generic + )) (native-inputs - `(;("java-findbugs-annotations" ,java-findbugs-annotations) - ;("java-findbugs-jsr305" ,java-findbugs-jsr305) - ;("java-jumble-annotations" ,java-jumble-annotations) - ;; for tests - ("java-hamcrest-core" ,java-hamcrest-core) - ("java-junit" ,java-junit) - ;("java-spelling" ,java-spelling) - ("unzip" ,unzip))) + (list ;java-findbugs-annotations + ;java-findbugs-jsr305 + ;java-jumble-annotations + ;; for tests + java-hamcrest-core + java-junit + ;java-spelling + ;; For the 'install phase. + unzip)) (home-page "https://github.com/RealTimeGenomics/rtg-tools/") (synopsis "Utilities for accurate VCF comparison and manipulation") (description "RTG Tools is a subset of RTG Core that includes several useful diff --git a/gn/packages/javascript.scm b/gn/packages/javascript.scm index 7be9db4..7f9f35d 100644 --- a/gn/packages/javascript.scm +++ b/gn/packages/javascript.scm @@ -433,6 +433,7 @@ tables with minimal effort.") (description "Scroller is a virtual rendering plug-in for DataTables which allows large datasets to be drawn on screen very quickly. Virtual rendering means is that only the visible portion of the table is drawn, while the scrolling container gives the visual impression that the whole table is visible, allowing excellent browser performance.") (license license:expat))) + (define-public javascript-xterm (package (name "javascript-xterm") @@ -445,7 +446,7 @@ tables with minimal effort.") (file-name (string-append "xterm.min" version ".js")) (sha256 (base32 - "18smra546ws5fhnfdhj9m6yhvfjqdwx44jyb19q3az780ifwj2lz")))) + "1ipk8l837pinl9151qcb39hfrjy5d7zzyf19nsfhv4wgavy8fcar")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -458,7 +459,7 @@ tables with minimal effort.") (source (assoc-ref %build-inputs "source"))) (mkdir-p targetdir) (copy-file source (string-append targetdir "/xterm.min.js")))))) - (native-inputs `(("source" ,source))) + (propagated-inputs `(("source" ,source))) (home-page "https://xtermjs.org/") (synopsis "Javascript library that allows apps to bring fully-featured terminals in browsers.") (description @@ -805,6 +806,41 @@ without tying yourself to a proprietary framework, combining powerful visualization components and a data-driven approach to DOM manipulation.") (license license:bsd-3))) +(define-public javascript-d3panels + (package + (name "javascript-d3panels") + (version "1.8.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/kbroman/d3panels.git") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1pmv24x4k0iy2mbibwwk8f85c6mljyqj2qwn03sq3pg93r16a0b5")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (targetdir (string-append out "/share/genenetwork2/javascript/d3panels")) + (source (assoc-ref %build-inputs "source"))) + (install-file (string-append source "/d3panels.js") targetdir) + (install-file (string-append source "/d3panels.min.js") targetdir) + (install-file (string-append source "/d3panels.css") targetdir) + (install-file (string-append source "/d3panels.min.css") targetdir) + (install-file (string-append source "/README.md") targetdir) + (install-file (string-append source "/NEWS.md") targetdir) + (install-file (string-append source "/LICENSE.md") targetdir) + )))) + (home-page "https://kbroman.org/d3panels") + (synopsis "d3panels for QTL mapping") + (description "This is a set of D3-based graphic panels, to be combined into larger multi-panel charts. They were developed for the R/qtlcharts package.") + (license license:expat))) + (define-public javascript-jquery (package (inherit web-jquery) @@ -858,6 +894,46 @@ visualization components and a data-driven approach to DOM manipulation.") (install-file "d3.min.js" targetdir) (install-file "LICENSE" (string-append out "/share/doc/d3js-" ,version)))))))) +(define-public javascript-d3js-7 + (package + (name "javascript-d3js-7") + (version "7.9.0") + (source + (origin + (method url-fetch) + ;; note that D3 no longer provides a prebuilt JS file - except through CDS + (uri (string-append "https://files.genenetwork.org/software/d3.v" version ".min.js.gz")) + (sha256 + (base32 "0k7g40zb65s12z1zchvimj5xibkrqff5sylbrhcwmwpcplpigid7")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (module-name "d3js-7") + (gzip (string-append (assoc-ref %build-inputs "gzip") + "/bin/gzip")) + (targetdir (string-append out "/share/genenetwork2/javascript/" module-name)) + (jsname (string-append "d3.v" "7.9.0" ".min.js")) + (gzname (string-append jsname ".gz")) + (source (assoc-ref %build-inputs "source"))) + (mkdir-p targetdir) + (copy-file (pk source) (pk (string-append targetdir "/" gzname))) + (invoke gzip "-fd" (string-append targetdir "/" gzname)))))) + (native-inputs + `(("source" ,source) + ("gzip" ,gzip))) + (home-page "https://d3js.org/") + (synopsis "JavaScript library for visualizing data") + (description "D3.js is a JavaScript library for manipulating documents based +on data. D3 helps you bring data to life using HTML, SVG, and CSS. D3's +emphasis on web standards gives you the full capabilities of modern browsers +without tying yourself to a proprietary framework, combining powerful +visualization components and a data-driven approach to DOM manipulation.") + (license license:bsd-3))) + (define-public javascript-d3js-multi (package (name "javascript-d3js-multi") @@ -1319,32 +1395,37 @@ a sample function, allowing for more complex calculations.") (arguments `(#:javascript-files '("dist/jstat.js"))) (build-system minify-build-system))) -(define-public javascript-ckeditor ; version 4 +(define-public javascript-ckeditor ; version 4 (package (name "javascript-ckeditor") - (version "4.13.0") ; Sept. 26, 2019 + (version "4.13.0") ; Sept. 26, 2019 (source (origin (method url-fetch) - (uri (string-append "https://cdn.ckeditor.com/" version - "/standard/ckeditor.js")) - (file-name (string-append "ckeditor-" version ".js")) + (uri (string-append "http://download.cksource.com/CKEditor/CKEditor/CKEditor%20" version + "/ckeditor_4.13.0_standard.zip")) (sha256 - (base32 - "0cvf1qdva5h2dh8y10c9v7dxrd82siswxx7h6cq0mf46ssjdygd0")))) + (base32 + "1n2xynmbr2v4wm2g2vqcqd16n93phsbq4sqrnljzb7wzjq9svl36")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) #:builder (begin - (use-modules (guix build utils)) - (let* ((out (assoc-ref %outputs "out")) - (targetdir - (string-append out "/share/genenetwork2/javascript/ckeditor")) - (source (assoc-ref %build-inputs "source"))) - (mkdir-p targetdir) - (copy-file source (string-append targetdir "/ckeditor.js")))))) - (native-inputs `(("source" ,source))) + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (name "ckeditor") + (unzip (string-append (assoc-ref %build-inputs "unzip") + "/bin/unzip")) + (targetdir + (string-append (string-append out "/share/genenetwork2/javascript/" name))) + (source (assoc-ref %build-inputs "source"))) + (mkdir-p targetdir) + (invoke unzip source) + (copy-recursively "ckeditor" targetdir))))) + (native-inputs + `(("source" ,source) + ("unzip" ,unzip))) (home-page "https://ckeditor.com/") (synopsis "Smart WYSIWYG HTML editor") (description @@ -1358,8 +1439,8 @@ browser compatibility, including legacy browsers. @item Long-term support (LTS) until 2023. @end enumerate") (license (list license:gpl2+ - license:lgpl2.1+ - license:mpl1.1)))) ; Any of these three + license:lgpl2.1+ + license:mpl1.1)))) ; Any of these three (define-public javascript-parsley (package @@ -1849,7 +1930,7 @@ Popper will automatically put the tooltip in the right place near the button.") (define-public javascript-font-awesome (package (name "javascript-font-awesome") - (version "5.15.2") + (version "v4.7.0") (source (origin (method git-fetch) @@ -1858,7 +1939,7 @@ Popper will automatically put the tooltip in the right place near the button.") (commit version))) (file-name (git-file-name name version)) (sha256 - (base32 "1jin0qlf5lv4l9gj8qc1pp34mxyvyj6gma4qnjqiah1bzcfn635l")))) + (base32 "0w30y26jp8nvxa3iiw7ayl6rkza1rz62msl9xw3srvxya1c77grc")))) (build-system trivial-build-system) (arguments `(#:modules ((guix build utils)) @@ -1868,16 +1949,232 @@ Popper will automatically put the tooltip in the right place near the button.") (let* ((out (assoc-ref %outputs "out")) (targetdir (string-append out "/share/genenetwork2/javascript/fontawesome")) (source (assoc-ref %build-inputs "source")) - (js-dir (string-append source "/js")) (css-dir (string-append source "/css")) - (fonts-dir (string-append source "/webfonts"))) + (fonts-dir (string-append source "/fonts"))) (copy-recursively css-dir (string-append targetdir "/css")) - (copy-recursively js-dir (string-append targetdir "/js")) (copy-recursively fonts-dir - (string-append targetdir "/webfonts")))))) + (string-append targetdir "/fonts")))))) (native-inputs `(("source" ,source))) (home-page "https://fontawesome.com/") (synopsis "Font that contains a rich iconset") (description "Font Awesome is a full suite of pictographic icons for easy scalable vector graphics.") (license license:silofl1.1))) + + +(define-public javascript-htmx + (package + (name "javascript-htmx") + (version "1.9.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bigskysoftware/htmx") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "14m9wan8sp5lzblfzbi1hln621p7ld3npajxrhq1a19zm5bcrz3y")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((source (assoc-ref %build-inputs "source")) + (out (assoc-ref %outputs "out")) + (targetdir (string-append out "/share/genenetwork2/javascript"))) + (mkdir-p targetdir) + (copy-file (string-append source "/dist/htmx.min.js") + (string-append targetdir "/htmx.min.js")))))) + (home-page "https://htmx.org/") + (synopsis "High Power Tools for HTML") + (description + "htmx allows you to access AJAX, CSS Transitions, WebSockets and Server Sent Events directly in HTML, using attributes, so you can build modern user interfaces with the simplicity and power of hypertext") + (license license:expat))) + +(define-public javascript-marked + (package + (name "javascript-marked") + (version "9.1.5") + (source + (origin + (method url-fetch) + (uri (string-append "https://cdnjs.cloudflare.com/ajax/libs/marked/" version + "/marked.min.js")) + (file-name "marked.min.js") + (sha256 + (base32 + "1f4hw8yjdm99hgw0bq62099d3kv23awsm8r7969m7lv84n2wid8y")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (targetdir + (string-append out "/share/genenetwork2/javascript/marked")) + (source (assoc-ref %build-inputs "source"))) + (mkdir-p targetdir) + (copy-file source (string-append targetdir "/marked.min.js")))))) + (native-inputs `(("source" ,source))) + (home-page "https://marked.js.org/") + (synopsis "A markdown parser and compiler. Built for speed.") + (description + "A low-level markdown compiler for parsing markdown without caching or blocking for long periods of time.") + (license license:expat))) + +(define-public javascript-marked-highlight + (package + (name "javascript-marked-highlight") + (version "2.0.6") + (source + (origin + (method url-fetch) + (uri (string-append "https://cdn.jsdelivr.net/npm/marked-highlight@" version "/lib/index.umd.min.js")) + (sha256 + (base32 + "087qcy77fm3r7dl6w0mxsqygmdpimrmksw78r4wkkkjdx9x9dshf")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (targetdir + (string-append out "/share/genenetwork2/javascript/marked")) + (source (assoc-ref %build-inputs "source"))) + (mkdir-p targetdir) + (copy-file source (string-append targetdir "/marked-highlight.js")))))) + (native-inputs `(("source" ,source))) + (home-page "https://github.com/markedjs/marked-highlight") + (synopsis "Highlight code blocks.") + (description + "Add code highlighting to marked.") + (license license:expat))) + +(define-public javascript-ace + (package + (name "javascript-ace") + (version "1.31.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ajaxorg/ace-builds.git") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "08rfyrjfjjgb42x4if5qqfyvv8ag2qmf6vsbs7qrcnzgrac66m35")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (targetdir (string-append out "/share/genenetwork2/javascript/ace")) + (source (assoc-ref %build-inputs "source")) + (dist (string-append source "/src-min-noconflict"))) + (copy-recursively dist targetdir))))) + (native-inputs `(("source" ,source))) + (home-page "https://github.com/ajaxorg/ace-builds") + (synopsis "Ace is a code editor written in JavaScript.") + (description + "Ace is a code editor written in JavaScript. ") + (license license:expat))) + +(define-public javascript-uikit + (package + (name "javascript-uikit") + (version "3.7.4") + (source + (origin + (method url-fetch) + (uri (string-append "https://github.com/uikit/uikit/releases/download/v" + version "/uikit" "-" version ".zip")) + (sha256 + (base32 "1qhhz3iki1nbyffg6qa7x2937708hjr9gf6mkn4v4cdl9j0mgyv0")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (unzip (string-append (assoc-ref %build-inputs "unzip") + "/bin/unzip")) + (targetdir (string-append out "/share/genenetwork2/javascript/uikit")) + (source (assoc-ref %build-inputs "source"))) + (invoke unzip source) + (copy-recursively "." targetdir))))) + (native-inputs + `(("source" ,source) + ("unzip" ,unzip))) + (home-page "https://getuikit.com/") + (synopsis "UIkit is a lightweight and modular front-end framework +for developing fast and powerful web interfaces.") + (description "UIkit is a lightweight and modular front-end framework +for developing fast and powerful web interfaces.") + (license license:bsd-3))) + +(define-public javascript-linkify + (package + (name "javascript-linkify") + (version "4.1.3") + (source + (origin + (method url-fetch) + (uri (string-append "https://cdn.jsdelivr.net/npm/linkifyjs@" version "/dist/linkify.min.js")) + (sha256 + (base32 + "1cy1z4gin0qx3a04fw2biszz1sgns0zc1zbr6sbkr2dicgqxjpf3")))) + (build-system trivial-build-system) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (targetdir + (string-append out "/share/genenetwork2/javascript/linkify")) + (source (assoc-ref %build-inputs "source"))) + (mkdir-p targetdir) + (copy-file source (string-append targetdir "/linkify.min.js")))))) + (native-inputs `(("source" ,source))) + (home-page "https://linkify.js.org") + (synopsis "Find URLs and email addresses in plain text") + (description + "JavaScript plugin for finding links in plain-text and converting them to HTML <a> tags") + (license license:expat))) + +(define-public javascript-linkify-html + (package + (inherit javascript-linkify) + (name "javascript-linkify-html") + (version "4.1.3") + (source + (origin + (method url-fetch) + (uri (string-append "https://cdn.jsdelivr.net/npm/linkify-html@" version "/dist/linkify-html.min.js")) + (sha256 + (base32 + "1s3l4wnyws9c9qjgp9ivl88inhyy28cjrhqjayb6hm1hzkasgj2j")))) + (arguments + `(#:modules ((guix build utils)) + #:builder + (begin + (use-modules (guix build utils)) + (let* ((out (assoc-ref %outputs "out")) + (targetdir + (string-append out "/share/genenetwork2/javascript/linkify")) + (source (assoc-ref %build-inputs "source"))) + (mkdir-p targetdir) + (copy-file source (string-append targetdir "/linkify-html.min.js")))))) + (native-inputs `(("source" ,source))) + (description + "JavaScript plugin for finding links in plain-text and highlightinging links within strings that contain HTML markup.") + (license license:expat))) diff --git a/gn/packages/julia.scm b/gn/packages/julia.scm index 31cc29c..a00244f 100644 --- a/gn/packages/julia.scm +++ b/gn/packages/julia.scm @@ -17,6 +17,7 @@ #:use-module (gnu packages julia-xyz) #:use-module (gnu packages python) #:use-module (gnu packages statistics) + #:use-module (gnu packages version-control) #:use-module (gnu packages video) #:use-module (ice-9 match)) @@ -24,7 +25,7 @@ (define-public julia-visuals (let ((commit "e8e2b601f40a76c8f20f0ddfe80c56257dd9a294") - (revision "2")) + (revision "3")) (package (name "julia-visuals") (version (git-version "0.0.0" revision commit)) @@ -51,6 +52,7 @@ (replace 'install (lambda* (#:key outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) + (mkdir-p (string-append out "/bin")) ;; Copied from the Dockerfile. (for-each (lambda (file) @@ -59,6 +61,7 @@ "environment.yml" "setup.py" "runpluto.sh" + "runsliderserver.sh" "notebooks" "Project.toml"))))) (add-after 'install 'wrap-program @@ -68,11 +71,15 @@ (wrap-script (string-append out "/runpluto.sh") `("PATH" ":" prefix (,(string-append (assoc-ref inputs "julia") "/bin") ,(string-append (assoc-ref inputs "coreutils") "/bin"))) + `("JULIA_LOAD_PATH" ":" prefix (,(getenv "JULIA_LOAD_PATH")))) + (wrap-script (string-append out "/runsliderserver.sh") + `("PATH" ":" prefix (,(string-append (assoc-ref inputs "julia") "/bin") + ,(string-append (assoc-ref inputs "coreutils") "/bin"))) `("JULIA_LOAD_PATH" ":" prefix (,(getenv "JULIA_LOAD_PATH"))))))) - (add-after 'install 'create-run-program + (add-after 'install 'create-runpluto (lambda* (#:key inputs outputs #:allow-other-keys) (let ((out (assoc-ref outputs "out"))) - (with-output-to-file (string-append out "/runpluto") + (with-output-to-file (string-append out "/bin/runpluto") (lambda () (format #t "#!~a --no-auto-compile !# @@ -93,25 +100,64 @@ (getenv "JULIA_LOAD_PATH") (dirname (search-input-file inputs "/bin/yes")) (search-input-file inputs "/bin/julia")))) - (chmod (string-append out "/runpluto") #o555)))) + (chmod (string-append out "/bin/runpluto") #o555)))) + (add-after 'install 'create-runsliderserver + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (with-output-to-file (string-append out "/bin/runsliderserver") + (lambda () + (format #t "#!~a --no-auto-compile +!# +(setenv \"JULIA_LOAD_PATH\" \"~a\") +(setenv \"PATH\" \"~a\") +;; First initialise or update the julia registry: +(zero? (system* \"~a\" + \"--optimize=0\" + ;; Used by L1-penalty.jl: + ;; \"-e\" \"import Pkg; Pkg.add(\\\"PlotlyBase\\\")\" + \"-e\" \"import Pkg; Pkg.update()\")) +(zero? (system* \"~a\" + \"--optimize=0\" + \"-e\" \"import PlutoSliderServer; + PlutoSliderServer.run_directory( + \\\"~a/notebooks/\\\", + SliderServer_port=4343, + SliderServer_host=\\\"0.0.0.0\\\")\"))\n" + (search-input-file inputs "/bin/guile") + (getenv "JULIA_LOAD_PATH") + (dirname (search-input-file inputs "/bin/yes")) + (search-input-file inputs "/bin/julia") + (search-input-file inputs "/bin/julia") + out))) + (chmod (string-append out "/bin/runsliderserver") #o555)))) (replace 'precompile (lambda _ (invoke "julia" "-e" "\"import Pkg; Pkg.instantiate(); Pkg.status(); Pkg.precompile()\"")))))) + #; (propagated-inputs + ;; This doesn't seem to actually be used anywhere `(;; from setup.py ("python-jupyter-server-proxy" ,(@ (gn packages python) python-jupyter-server-proxy-1)))) (inputs - (list julia-distributions + ;; Ideally we'd use more of these packages, but we end up downloading + ;; most of them anyway when the service starts, so we've commented them + ;; out for now. + (list ;julia-cairomakie ; 0.8.13 + ;julia-distributions ; 0.25.76 ;julia-interactiveutils ; stdlib - julia-latexstrings + ;julia-latexstrings ; 1.3.0 ;julia-markdown ; stdlib - julia-optim - julia-plots - julia-pluto - julia-plutoui + ;julia-optim ; 1.7.2 + ;julia-plots ; 1.35.3 + ;julia-pluto ; 0.19.11 + julia-plutosliderserver ; * + ;julia-plutoui ; 0.7.46 + ;julia-prettytables ; 2.1.0 + ;julia-quadgk ; 2.5.0 + ;julia-roots ; 2.0.3 (@ (gnu packages guile) guile-3.0))) ; for wrap-script (home-page "https://github.com/sens/visuals") (synopsis "Visualizations using Pluto.jl notebooks") @@ -302,25 +348,35 @@ distributed computing.") (base32 "0nqlnkh8grxfm8d1mivi7dnrvb31bznj9s540a10d2v396ikfggn")))) (build-system julia-build-system) (arguments - `(#:tests? #f)) ; Some failed tests + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'adjust-tests + (lambda _ + ;; Something about logpdf fails in both of these test sets. + (substitute* "test/multivariate/dirichlet.jl" + (("\\@testset \"_logpdf\" begin") + "@testset \"_logpdf\" begin return;")) + (substitute* "test/univariate/discrete/negativebinomial.jl" + ;; The negative numbers something something wrong in logpdf. + (("0, 10, 42, -1, -5, -13") "0, 10, 42"))))))) (propagated-inputs - `(("julia-chainrulescore" ,julia-chainrulescore) - ("julia-densityinterface" ,julia-densityinterface) - ("julia-fillarrays" ,julia-fillarrays) - ("julia-pdmats" ,julia-pdmats) - ("julia-quadgk" ,julia-quadgk) - ("julia-specialfunctions" ,julia-specialfunctions) - ("julia-statsbase" ,julia-statsbase) - ("julia-statsfuns" ,julia-statsfuns))) + (list julia-chainrulescore ; 1 + julia-densityinterface ; 0.4 + julia-fillarrays ; 0.9 .. 0.13 + julia-pdmats ; 0.10, 0.11 + julia-quadgk ; 2 + julia-specialfunctions ; 1.2, 2 + julia-statsbase ; 0.32, 0.33 + julia-statsfuns)) ; 0.9.15, 1 (native-inputs - `(("julia-calculus" ,julia-calculus) - ("julia-chainrulestestutils" ,julia-chainrulestestutils) - ("julia-finitedifferences" ,julia-finitedifferences) - ("julia-forwarddiff" ,julia-forwarddiff) - ("julia-json" ,julia-json) - ("julia-offsetarrays" ,julia-offsetarrays) - ("julia-stablerngs" ,julia-stablerngs) - ("julia-staticarrays" ,julia-staticarrays))) + (list julia-calculus + julia-chainrulestestutils + julia-finitedifferences + julia-forwarddiff + julia-json + julia-offsetarrays + julia-stablerngs + julia-staticarrays)) (home-page "https://github.com/JuliaStats/Distributions.jl") (synopsis "Probability distributions and associated functions") (description "Julia package for probability distributions and associated @@ -335,6 +391,302 @@ properties @end enumerate") (license license:expat))) +(define-public julia-fromfile + (package + (name "julia-fromfile") + (version "0.1.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Roger-luo/FromFile.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0jn394294d4s1fqsfiwpiy6dzlca4ciy54l2xviwyzhvixmlfrwn")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f)) ; Tests require network access + (propagated-inputs + (list julia-requires)) + (home-page "https://github.com/Roger-luo/FromFile.jl") + (synopsis "Julia enhancement proposal for implicit per file module in Julia") + (description "This package exports a macro @code{@@from}, which can be used +to import objects from files.") + (license license:expat))) + +(define-public julia-git + (package + (name "julia-git") + (version "1.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaVersionControl/Git.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0bznzg360cbvbzzpsdkin4dm2v980sb5pv58gy1bp3j9j8bj38h6")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-network-tests + (lambda _ + (substitute* "test/runtests.jl" + (("testset.*Git.jl.*" all) + (string-append all " return\n")))))))) + (propagated-inputs + (list julia-git-jll)) + (home-page "https://github.com/JuliaVersionControl/Git.jl") + (synopsis "Use command-line Git in your Julia packages") + (description "Git.jl allows you to use command-line Git in your Julia +packages. You do not need to have Git installed on your computer, and neither +do the users of your packages!") + (license license:expat))) + +(define-public julia-git-jll + (package + (name "julia-git-jll") + (version "2.36.1+2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaBinaryWrappers/Git_jll.jl") + (commit (string-append "Git-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1n8k363q2mw5qfkagbbqpn4djx181qbn05l7brp3spspvf5aslgm")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'link-depot 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"Git\", \"" + (assoc-ref inputs "git-minimal") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + (list git-minimal)) + (propagated-inputs + (list julia-jllwrappers + julia-expat-jll + julia-openssl-jll + ;julia-libcurl-jll + julia-libiconv-jll + ;julia-pcre2-jll + julia-zlib-jll)) + (home-page "https://github.com/JuliaBinaryWrappers/Git_jll.jl") + (synopsis "Git library wrappers") + (description "This package provides a wrapper for the git library.") + (license license:expat))) + +(define-public julia-glob + (package + (name "julia-glob") + (version "1.3.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vtjnash/Glob.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "05yp7ba3y3pfibs0hy2sp61phb5b6x7aacsjc93i3lz6wmlpj0jx")))) + (build-system julia-build-system) + (home-page "https://github.com/vtjnash/Glob.jl") + (synopsis "Posix-compliant file name pattern matching") + (description "This implementation of Glob is based on the IEEE Std 1003.1, +2004 Edition (Open Group Base Specifications Issue 6) for fnmatch and glob.") + (license license:expat))) + +(define-public julia-terminalloggers + (package + (name "julia-terminalloggers") + (version "0.1.7") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaLogging/TerminalLoggers.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "01l9qsjljwa9pkpvf1pafmbrncjddwdw3737pf44y9q5hrp4hbr7")))) + (build-system julia-build-system) + (propagated-inputs + (list julia-leftchildrightsiblingtrees + julia-progresslogging)) + (home-page "https://github.com/JuliaLogging/TerminalLoggers.jl") + (synopsis "Logging sinks and utilites for interactive terminals") + (description "TerminalLoggers provides a logger type @code{TerminalLogger} +which can format your log messages in a richer way than the default +@code{ConsoleLogger} which comes with the julia standard @code{Logging} +library.") + (license license:expat))) + +(define-public julia-roots + (package + (name "julia-roots") + (version "2.0.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaMath/Roots.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "17d62r8pib3cp73az00iz8nbnd5j0y3dl1mrmcssnj4ln8043056")))) + (build-system julia-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-expensive-tests + (lambda _ + (substitute* "test/runtests.jl" + ((".*test_composable.*") ""))))))) + (propagated-inputs + (list julia-commonsolve + julia-setfield)) + (native-inputs + (list julia-benchmarktools + julia-forwarddiff + julia-json + julia-specialfunctions)) + (home-page "http://juliamath.github.io/Roots.jl/") + (synopsis "Root finding functions for Julia") + (description "This package contains simple routines for finding roots, or +zeros, of scalar functions of a single real variable using floating-point +math.") + (license license:expat))) + +(define-public julia-commonsolve + (package + (name "julia-commonsolve") + (version "0.2.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/SciML/CommonSolve.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1w05fp02g5cmqzqp96hcpriwjpqx61sl481rj92gf4y4xpinmdf5")))) + (build-system julia-build-system) + (home-page "https://docs.sciml.ai/CommonSolve/stable") + (synopsis "Common solve function for scientific machine learning") + (description "This holds the common @code{solve}, @code{init}, +@code{step!}, and @code{solve!} commands. By using the same definition, solver +libraries from other completely different ecosystems can extend the functions +and thus not clash with SciML if both ecosystems export the @code{solve} +command. The rules are that you must dispatch on one of your own types.") + (license license:expat))) + +(define-public julia-setfield + (package + (name "julia-setfield") + (version "1.1.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/jw3126/Setfield.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0vdn9s639f120560599m4lhqkk0nsx7qa87fv2mixs1faaihsf6l")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f)) ; Skip tests, not all dependencies packaged. + (propagated-inputs + (list julia-constructionbase + julia-macrotools + julia-staticarrayscore)) + (home-page "https://github.com/jw3126/Setfield.jl") + (synopsis "Update deeply nested immutable structs") + (description "Update deeply nested immutable structs.") + (license license:expat))) + +(define-public julia-staticarrayscore + (package + (name "julia-staticarrayscore") + (version "1.4.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaArrays/StaticArraysCore.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0m573mxvf0y9h7y8rxrk35haphhqisplx159r77g30qvw7zwpgar")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaArrays/StaticArraysCore.jl") + (synopsis "Interface package for StaticArrays.jl") + (description + "This package provides an interface package for @code{StaticArrays.jl}.") + (license license:expat))) + +(define-public julia-progresslogging + (package + (name "julia-progresslogging") + (version "0.1.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaLogging/ProgressLogging.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ysixnl7wjdykaka892jrhsay2aivpch83h8dnfs43z2xynf9sqn")))) + (build-system julia-build-system) + (native-inputs + (list julia-offsetarrays)) + (home-page "https://github.com/JuliaLogging/ProgressLogging.jl") + (synopsis "Define progress logs") + (description "ProgressLogging.jl is a package for defining progress logs. +It can be used to report progress of a loop/loops with time-consuming body.") + (license license:expat))) + +(define-public julia-leftchildrightsiblingtrees + (package + (name "julia-leftchildrightsiblingtrees") + (version "0.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaCollections/LeftChildRightSiblingTrees.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1rijr0yqmbzhlk668v4rqw5xmxxzqvgziasyqrd6z837376mfyy6")))) + (build-system julia-build-system) + (propagated-inputs + (list julia-abstracttrees)) + (home-page "https://github.com/JuliaCollections/LeftChildRightSiblingTrees.jl") + (synopsis "Representation of a tree with arbitrary number of children/node") + (description "A left child, right sibling tree (frequently abbreviated as +\"LCRS\") is a rooted tree data structure that allows a parent node to have +multiple child nodes. Rather than maintain a list of children (which requires +one array per node), instead it is represented as a binary tree, where the +\"left\" branch is the first child, whose \"right\" branch points to its first +sibling.") + (license license:expat))) + ;; ready to upstream (define-public julia-densityinterface (package @@ -363,7 +715,7 @@ densities and objects associated with a density in Julia.") (define-public julia-plots (package (name "julia-plots") - (version "1.16.6") + (version "1.35.6") (source (origin (method git-fetch) @@ -372,57 +724,610 @@ densities and objects associated with a density in Julia.") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0ipv9408r4czsx1j01sv2f7ww52b329jc0v79npn4x2mf827nsik")))) + (base32 "005za8a8al822xr0cz4yi1rm23qj1lzy9iw93vvhwq76x3n8bfpy")))) (build-system julia-build-system) (arguments `(#:tests? #f ; for now + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'adjust-tests + (lambda _ + ;; Decrease the number of tests we're running. + (substitute* "test/runtests.jl" + ((".*VisualRegressionTests.*") "") + ((".*pgfplotsx.*") "") + ((".*plotlyjs.*") "") + )))) )) (propagated-inputs - `( - ;("julia-contour" ,julia-contour) - ("julia-ffmpeg" ,julia-ffmpeg) - ("julia-fixedpointnumbers" ,julia-fixedpointnumbers) - ("julia-gr" ,julia-gr) - ("julia-geometrybasics" ,julia-geometrybasics) - ("julia-json" ,julia-json) - ;("julia-latexify" ,julia-latexify) - ("julia-measures" ,julia-measures) - ("julia-nanmath" ,julia-nanmath) - ("julia-plotthemes" ,julia-plotthemes) - ("julia-plotutils" ,julia-plotutils) - ("julia-recipesbase" ,julia-recipesbase) - ("julia-recipespipeline" ,julia-recipespipeline) - ("julia-reexport" ,julia-reexport) - ("julia-requires" ,julia-requires) - ("julia-scratch" ,julia-scratch) - ("julia-showoff" ,julia-showoff) - ("julia-statsbase" ,julia-statsbase) - )) + (list julia-contour + julia-ffmpeg + julia-fixedpointnumbers + julia-gr + julia-geometrybasics + julia-jlfzf + julia-json + ;julia-latexify + julia-measures + julia-nanmath + julia-plotthemes + julia-plotutils + julia-recipesbase + julia-recipespipeline + julia-reexport + julia-relocatablefolders + julia-requires + julia-scratch + julia-showoff + julia-snoopprecompile + julia-statsbase + julia-unicodefun + julia-unzip)) (native-inputs - `( - ;("julia-distributions" ,julia-distributions) - ("julia-fileio" ,julia-fileio) - ;("julia-gtk" ,julia-gtk) - ;("julia-hdf5" ,julia-hdf5) - ("julia-imagemagick" ,julia-imagemagick) - ;("julia-images" ,julia-images) - ("julia-offsetarrays" ,julia-offsetarrays) - ;("julia-pgfplotsx" ,julia-pgfplotsx) - ;("julia-plotlyjs" ,julia-plotlyjs) - ;("julia-rdatasets" ,julia-rdatasets) - ("julia-stablerngs" ,julia-stablerngs) - ("julia-staticarrays" ,julia-staticarrays) - ;("julia-statsplots" ,julia-statsplots) - ("julia-testimages" ,julia-testimages) - ;("julia-unicodeplots" ,julia-unicodeplots) - ;("julia-visualregressiontests" ,julia-visualregressiontests) - )) + (list julia-aqua + julia-colors + ;julia-conda + julia-distributions + julia-fileio + julia-filepathsbase + ;julia-gaston + julia-geometrybasics + ;julia-gtk + ;julia-hdf5 + julia-imagemagick + ;julia-images + ;julia-inspectdr + julia-offsetarrays + ;julia-pgfplotsx + ;julia-plotlybase + ;julia-plotlyjs + ;julia-plotlykaleido + julia-pycall + julia-pyplot + ;julia-rdatasets + julia-sentinelarrays + julia-stablerngs + julia-staticarrays + ;julia-statsplots + julia-testimages + julia-unicodeplots + julia-unitful + ;julia-visualregressiontests + )) (home-page "http://docs.juliaplots.org/") (synopsis "Powerful convenience for Julia visualizations and data analysis") (description "Plots is a plotting API and toolset.") (license license:expat))) +(define-public julia-contour + (package + (name "julia-contour") + (version "0.5.7") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGeometry/Contour.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ai6lh5ap9qxhqm2k1pnkfbpm4b95d3v7izhyvrr9cxwbxfjv3vn")))) + (build-system julia-build-system) + (arguments `(#:tests? #f)) ;; FIX ME + (propagated-inputs + (list julia-staticarrays)) + (native-inputs + (list julia-offsetarrays + julia-statsbase)) + (home-page "https://github.com/JuliaGeometry/Contour.jl") + (synopsis "Calculating contour curves for 2D scalar fields in Julia") + (description "This package provides a generic implementation of the +@url{https://en.wikipedia.org/wiki/Marching_squares, marching squares} +algorithm for tracing contour curves on a scalar 2D field.") + (license license:expat))) + +(define-public julia-unicodeplots + (package + (name "julia-unicodeplots") + (version "2.12.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaPlots/UnicodePlots.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0plkczznx1297m1lviczkm4873yl29anr5csgyhh9vnvyf1606y2")))) + (build-system julia-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-tests + (lambda _ + ;; It is unclear why these tests fail and why some + ;; have a suprise dependency on AstroIO (from FileIO) + (substitute* "test/runtests.jl" + ((".*tst_world_age.*") "") + ((".*tst_io.*") "") + ((".*tst_densityplot.*") "")) + (substitute* "test/tst_canvas.jl" + ((".*HeatmapCanvas, \"heatmap\".*") "")) + (substitute* "test/tst_histogram.jl" + (("testset.*keyword.*" all) + (string-append all " return;\n")) + (("testset.*vertical\".*" all) + (string-append all " return;\n"))) + (substitute* "test/tst_barplot.jl" + (("testset.*maximum.*" all) + (string-append all " return;\n"))) + (substitute* "test/tst_spy.jl" + (("testset.*parameters.*" all) + (string-append all " return;\n"))) + (substitute* "test/tst_boxplot.jl" + (("testset.*default.*" all) + (string-append all " return;\n")) + (("testset.*scaling.*" all) + (string-append all " return;\n"))) + (substitute* "test/tst_volume.jl" + (("testset.*cube.*" all) + (string-append all " return;\n")))))))) + (propagated-inputs + (list julia-colortypes + julia-contour + julia-crayons + julia-fileio + julia-freetypeabstraction + julia-lazymodules + julia-marchingcubes + julia-nanmath + julia-staticarrays + julia-statsbase + julia-unitful)) + (native-inputs + (list julia-colortypes + julia-imagemagick + julia-referencetests + julia-stablerngs)) + (home-page "https://github.com/JuliaPlots/UnicodePlots.jl") + (synopsis "Unicode-based scientific plotting for working in the terminal") + (description "Advanced Unicode plotting library designed for use in Julia's REPL.") + (license license:expat))) + +(define-public julia-lazymodules + (package + (name "julia-lazymodules") + (version "0.3.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/johnnychen94/LazyModules.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "11xz0aw5w338pka9jf3r7mfhgm98fnqzsky5ig9z7b996z0m7lpk")))) + (build-system julia-build-system) + (native-inputs + (list julia-colors + julia-offsetarrays)) + (home-page "https://github.com/johnnychen94/LazyModules.jl") + (synopsis "Lazily load Julia modules") + (description "This package provides package developers an alternative +option to delay package loading until used. If some dependency is not used, +then users don't need to pay for its latency.") + (license license:expat))) + +(define-public julia-marchingcubes + (package + (name "julia-marchingcubes") + (version "0.1.8") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGeometry/MarchingCubes.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "14k47lz33j0fiashykf2a8ayiv482k5jkgw0iircw55mdkdrnxc3")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f)) ; Maybe later + (propagated-inputs + (list julia-precompiletools + julia-staticarrays)) + #; + (native-inputs + (list julia-benchmarktools + julia-geometrybasics + julia-meshes + julia-plyio)) + (home-page "https://github.com/JuliaGeometry/MarchingCubes.jl") + (synopsis "Efficient Implementation of Marching Cubes' Cases with Topological Guarantees") + (description "Julia port of Efficient Implementation of Marching Cubes' Cases with Topological Guarantees.") + (license license:expat))) + +(define-public julia-snoopprecompile + (package + (name "julia-snoopprecompile") + (version "1.0.3") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/timholy/SnoopCompile.jl") + (commit "v2.10.0"))) + (file-name (git-file-name name version)) + (sha256 + (base32 "14nnqknswjzlk786x4r7xc7898nmfk7ijfchrc09i81qi2d0mmcn")))) + (build-system julia-build-system) + (arguments + (list + #:tests? #f ; Most tests fail in the build environment. + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "SnoopPrecompile")))))) + (propagated-inputs + (list julia-preferences)) + (home-page "https://timholy.github.io/SnoopCompile.jl/dev/") + (synopsis "Effectively precompile code needed by your package") + (description "SnoopPrecompile is a small dependency used to effectively +precompile code needed by your package, particularly on Julia 1.8 and higher.") + (license license:expat))) + +(define-public julia-snoopcompile + (package + (name "julia-snoopcompile") + (version "1.7.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/timholy/SnoopCompile.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1xy0y5s7q980fl0kygvjbmn74i3sjpzbizsgvis70gd2fibz80h7")))) + (build-system julia-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-test-suite + (lambda _ + ;; This module fails to load its dependencies in the 'check phase. + (substitute* "test/runtests.jl" + ((".*snoopi\\.jl.*") "")) + (substitute* "test/snoopi.jl" + (("testset \"snoopi\" begin") + "testset \"snoopi\" begin return"))))))) + (propagated-inputs + (list julia-snoopcompileanalysis + julia-snoopcompilebot + julia-snoopcompilecore)) + (native-inputs + (list + ;julia-jld + ;julia-matlang + )) + (home-page "https://timholy.github.io/SnoopCompile.jl/dev/") + (synopsis "Making packages work faster with more extensive precompilation") + (description "SnoopCompile observes the Julia compiler, causing it to +record the functions and argument types it's compiling. From these lists of +methods, you can generate lists of @code{precompile} directives that may reduce +the latency between loading packages.") + (license license:expat))) + +(define-public julia-snoopcompileanalysis + (package/inherit julia-snoopcompile + (name "julia-snoopcompileanalysis") + (arguments + (list + #:tests? #f ; No test folder + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "SnoopCompileAnalysis")))))) + (propagated-inputs + (list julia-cthulhu + julia-orderedcollections)) + (native-inputs '()) + )) + +(define-public julia-snoopcompilebot + (package/inherit julia-snoopcompile + (name "julia-snoopcompilebot") + (arguments + (list + #:tests? #f ; Tests to be run in SnoopCompile.jl + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "SnoopCompileBot")))))) + (propagated-inputs + (list julia-filepathsbase + julia-snoopcompileanalysis + julia-snoopcompilecore + julia-yaml)) + (native-inputs '()) + )) + +(define-public julia-snoopcompilecore + (package/inherit julia-snoopcompile + (name "julia-snoopcompilecore") + (arguments + (list + #:tests? #f ; No test folder + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "SnoopCompileCore")))))) + (propagated-inputs '()) + (native-inputs '()) + )) + +(define-public julia-cthulhu + (package + (name "julia-cthulhu") + (version "1.6.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaDebug/Cthulhu.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1ziax1378kvyzikm4cigg4mq44r085zczqa0mkcbw5g36gcma6qi")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f)) ; Skip for now + (propagated-inputs + (list julia-codetracking + julia-foldingtrees)) + (native-inputs + (list julia-staticarrays)) + (home-page "https://github.com/JuliaDebug/Cthulhu.jl") + (synopsis "Slow descent into madness") + (description "Cthulhu can help you debug type inference issues by +recursively showing the @code{code_typed} output until you find the exact point +where inference gave up, messed up, or did something unexpected. Using the +Cthulhu interface you can debug type inference problems faster.") + (license license:expat))) + +(define-public julia-codetracking + (package + (name "julia-codetracking") + (version "1.3.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/timholy/CodeTracking.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0j6mclc7y1vpib5chj3hkabz9zbmdl76jgcr7314f5kbrdqjybbi")))) + (build-system julia-build-system) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'adjust-test-suite + (lambda _ + (substitute* "test/runtests.jl" + (("test pkgfiles\\(\"Color") + "test_skip pkgfiles\(\"Color"))))))) + (home-page "https://github.com/timholy/CodeTracking.jl") + (synopsis "It's editing-time, do you know where your methods are?") + (description "CodeTracking can be thought of as an extension of Julia's +InteractiveUtils library. It provides an interface for obtaining: +@enumerate +@item the strings and expressions of method definitions +@item the method signatures at a specific file & line number +@item location information for \"dynamic\" code that might have moved since it +was first loaded +@item a list of files that comprise a particular package.@end enumerate") + (license license:expat))) + +(define-public julia-foldingtrees + (package + (name "julia-foldingtrees") + (version "1.2.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaCollections/FoldingTrees.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1q3w44z1h9j22ykdwwgl8qdm9621m0qqwz4wd2rs2aj0921pdmm4")))) + (build-system julia-build-system) + (propagated-inputs + (list julia-abstracttrees)) + (home-page "https://github.com/JuliaCollections/FoldingTrees.jl") + (synopsis "Dynamic tree structure with control over the accessibility of node children") + (description "FoldingTrees implements a dynamic tree structure in which +some nodes may be \"folded,\" i.e., marked to avoid descent among that node's +children. It also supports interactive text menus based on folding trees.") + (license license:expat))) + +(define-public julia-jlfzf + (package + (name "julia-jlfzf") + (version "0.1.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Moelf/JLFzf.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0fvcx80lzj0xc4imb9h0iybj8s0cazjc1wn9h8xncih9aln25is4")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f)) ; no tests + (propagated-inputs + (list julia-fzf-jll + julia-pipe)) + (home-page "https://github.com/Moelf/JLFzf.jl") + (synopsis "Julia bind to fzf fuzzy finder") + (description "Julia bind to fzf fuzzy finder.") + (license license:expat))) + +(define-public julia-pipe + (package + (name "julia-pipe") + (version "1.3.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/oxinabox/Pipe.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "01anm76nfmcajcbr2piji0rknisf5wwhimfndwaadkqkcjv7k4xn")))) + (build-system julia-build-system) + (home-page "https://github.com/oxinabox/Pipe.jl") + (synopsis "Enhancement to Julia piping syntax") + (description "This package provides an enhancement to Julia piping syntax.") + (license license:expat))) + +(define-public julia-fzf-jll + (package + (name "julia-fzf-jll") + (version "0.35.1+0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/juliabinarywrappers/fzf_jll.jl") + (commit (string-append "fzf-v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0psl1lsvl6sza69g7qh8ha2ir89fibzid4ka3wzmjgh0r4yjfnw0")))) + (build-system julia-build-system) + (arguments + '(#:tests? #f ; no runtests + #:phases + (modify-phases %standard-phases + (add-after 'link-depot 'override-binary-path + (lambda* (#:key inputs #:allow-other-keys) + (map + (lambda (wrapper) + (substitute* wrapper + (("generate_wrapper_header.*") + (string-append + "generate_wrapper_header(\"fzf\", \"" + (assoc-ref inputs "fzf") "\")\n")))) + ;; There's a Julia file for each platform, override them all + (find-files "src/wrappers/" "\\.jl$"))))))) + (inputs + (list (@ (gnu packages terminals) fzf))) + (propagated-inputs + (list julia-jllwrappers)) + (home-page "https://github.com/JuliaBinaryWrappers/fzf_jll.jl") + (synopsis "Fzf library wrappers") + (description "This package provides a wrapper for fzf.") + (license license:expat))) + +(define-public julia-unicodefun + (package + (name "julia-unicodefun") + (version "0.4.1") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/SimonDanisch/UnicodeFun.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "11hch4zpi8qby8pcqfvxnx88y45lxan4ind9kj2d0pgw614zkpg0")))) + (build-system julia-build-system) + (home-page "https://github.com/SimonDanisch/UnicodeFun.jl") + (synopsis "Transform text into unicode symbols") + (description "This package offers a unicode transformation library.") + (license license:expat))) + +(define-public julia-unzip + (package + (name "julia-unzip") + (version "0.2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/bramtayl/Unzip.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0i4rkvyd8br024s0sgs3crpi6za2f51m42whkx0jd22wiwg675vb")))) + (build-system julia-build-system) + (native-inputs + (list julia-documenter)) + (home-page "https://github.com/bramtayl/Unzip.jl") + (synopsis "") + (description "") + (license license:expat))) + +;; Versions after 0.3.11 need a newer version of julia-http +(define-public julia-plutosliderserver + (package + (name "julia-plutosliderserver") + (version "0.3.11") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaPluto/PlutoSliderServer.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1aqc836glwqqs1pd9173sbjwjns3zv197xqdqlkp2xgrkjiw2yzg")))) + (build-system julia-build-system) + (arguments + `(#:tests? #f ; Tests require network access + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'adjust-source + (lambda _ + (setenv "GITHUB_ACTIONS" "false") + ;; Rip out betterfilewatching, it depends on a rust package. + (substitute* "src/PlutoSliderServer.jl" + ((".*watch_folder.*") "")) + ;; Remove GitHubActions + (substitute* "src/PlutoSliderServer.jl" + ((".*GitHubActions.*") ""))))))) + (propagated-inputs + (list julia-abstractplutodingetjes + ;julia-betterfilewatching ; should be disabled? + julia-configurations + julia-fromfile + julia-git + ;julia-githubactions ; can be disabled + julia-http + julia-json + julia-pluto + julia-terminalloggers)) + (home-page "https://github.com/JuliaPluto/PlutoSliderServer.jl") + (synopsis "Web server to run parts of a Pluto.jl notebook") + (description "This package provides a web server to run just the +@code{@@bind} parts of a @code{Pluto.jl} notebook.") + (license license:unlicense))) + ;; TODO: unbundle javascript calls to cdn.jsdelivr.net +;; The '-src' commit needs some nodejs packages to build the frontend. (define-public julia-pluto (package (name "julia-pluto") @@ -432,15 +1337,20 @@ densities and objects associated with a density in Julia.") (method git-fetch) (uri (git-reference (url "https://github.com/fonsp/Pluto.jl") - (commit (string-append "v" version "-src")))) + ;(commit (string-append "v" version "-src")))) + (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0h9sz4mpf3a4k0f5fblbb6j07wdhrnarxajrn0wz6zsq6w30x6yj")))) + ;(base32 "0h9sz4mpf3a4k0f5fblbb6j07wdhrnarxajrn0wz6zsq6w30x6yj")))) + (base32 "1qml5id3fi4r6n7hrqvfjwdvp3zp8xfckir3mw7vwswmkc56jzpq")))) (build-system julia-build-system) (arguments `(#:tests? #f ; Test suite tries to download the package registry. - #:phases - (modify-phases %standard-phases + ;#:phases + #;(modify-phases %standard-phases + #;(add-before 'check 'pre-check + (lambda _ + (setenv "PLUTO_TEST_ONLY_COMPILETIMES" "true"))) (add-after 'link-depot 'dont-check-for-upgrades (lambda _ (substitute* "frontend/components/welcome/Welcome.js" @@ -561,6 +1471,245 @@ native to Julia. Use it with the @code{@@bind} macro in Pluto.") (list julia-bufferedstreams julia-json)))) +(define-public julia-http-1.0 + (package + (inherit julia-http) + (name "julia-http") + (version "1.0.5") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaWeb/HTTP.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "15bqf0gv4qz3990cv1s2nj9mjqaka1pkhzymgwc19wxqvacwvwqr")))) + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-before 'install 'disable-network-tests + (lambda _ + (substitute* "test/runtests.jl" + (("\"async.jl") "# \"async.jl") + (("\"client.jl") "# \"client.jl") + (("\"websockets") "# \"websockets") + (("\"server") "# \"server")) + (substitute* "test/multipart.jl" + (("@testset \"Setting of Content-Type.*" all) + (string-append all "return\n")) + (("@testset \"Deprecation of .*" all) + (string-append all "return\n"))) + (substitute* "test/messages.jl" + (("@testset.*Read methods.*" all) + (string-append all "return\n")) + (("@testset.*Body - .*" all) + (string-append all "return\n")) + (("@testset.*Write to file.*" all) + (string-append all "return\n"))) + (substitute* "test/cookies.jl" + (("@testset.*Set-Cookie casing.*" all) + (string-append all "return\n"))) +))))) + (propagated-inputs + (list julia-codeczlib + julia-inifile + julia-loggingextras + julia-mbedtls + julia-simplebufferstream + julia-uris)) + ;; required for tests + (native-inputs + (list julia-bufferedstreams + julia-json)))) + +;; TODO: Unbundle fonts, more? +(define-public julia-makie + (package + (name "julia-makie") + (version "0.17.13") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/MakieOrg/Makie.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0s9rkfmshl3nz82zkgia6fxmfhz4v26ixam6ybqw8swlshdfijrd")))) + (build-system julia-build-system) + (propagated-inputs + (list ;julia-animations + ;julia-colorbrewer + julia-colorschemes + julia-colortypes + julia-colors + julia-contour + julia-distributions + julia-docstringextensions + julia-ffmpeg + julia-fileio + julia-fixedpointnumbers + julia-formatting + julia-freetype + julia-freetypeabstraction + julia-geometrybasics + ;julia-gridlayout + ;julia-imageio + julia-intervalsets + ;julia-isoband + ;julia-kerneldensity + julia-latexstrings + julia-makiecore + ;julia-match + ;julia-mathtexengine + julia-observables + julia-offsetarrays + ;julia-packing + julia-plotutils + ;julia-polygonops + julia-relocatablefolders + julia-showoff + ;julia-signeddistancefields + julia-statsbase + julia-statsfuns + julia-structarrays + julia-unicodefun)) + (home-page "https://docs.makie.org/stable") + (synopsis "Interactive data visualizations and plotting in Julia") + (description "Makie is a data visualization ecosystem for the Julia +programming language.") + (license license:expat))) + +(define-public julia-makiecore + (package/inherit julia-makie + (name "julia-makiecore") + (version "0.4.0") ; Same source, different version + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "MakieCore")))))) + (propagated-inputs + (list julia-observables)) + (synopsis "Backend core for Makie"))) + +(define-public julia-cairomakie + (package/inherit julia-makie + (name "julia-cairomakie") + (version "0.8.13") ; Same source, different version + (arguments + (list + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'chdir + (lambda _ + (chdir "CairoMakie")))))) + (propagated-inputs + (list ;julia-cairo + julia-colors + ;julia-fftw + julia-fileio + julia-freetype + julia-geometrybasics + julia-makie)) + (synopsis "Cairo Backend for Makie"))) + +(define-public julia-freetype + (package + (name "julia-freetype") + (version "4.1.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGraphics/FreeType.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "08kf1x1c7gvllds1ryv6zwy9ai85p50a509ndlcjrkiw31i612m8")))) + (build-system julia-build-system) + (propagated-inputs + (list julia-cenum + julia-freetype2-jll)) + (home-page "https://github.com/JuliaGraphics/FreeType.jl") + (synopsis "FreeType 2 bindings for Julia") + (description "This package provides FreeType bindings for Julia.") + (license license:zlib))) + +(define-public julia-freetypeabstraction + (package + (name "julia-freetypeabstraction") + (version "0.9.9") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGraphics/FreeTypeAbstraction.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0zqpwysvxjqh5lmsz7lysgyid7xnis23rr0xzn3fwxlncka7dbyl")) + (snippet + #~(begin + (use-modules (guix build utils)) + ;; Also find fonts in Guix environments. + (substitute* "src/findfonts.jl" + (("\"/usr/share/fonts\"," all) + (string-append all "\n " + "\"/run/current-system/profile/share/fonts\"," + "\n " + "joinpath(get(ENV, \"GUIX_ENVIRONMENT\", homedir())," + "\"share/fonts\")," + "\n " + "joinpath(get(ENV, \"GUIX_PROFILE\", homedir())," + "\"share/fonts\"),") )))))) + (build-system julia-build-system) + (arguments + (list + #:tests? #f ; Can't skip the one test as needed + #:phases + #~(modify-phases %standard-phases + (add-before 'check 'skip-findfont-test + (lambda _ + (substitute* "test/runtests.jl" + ;; Can't make this find font-dejavu + (("@test findfont\\(font") "@test_skip findfont(font"))))))) + (propagated-inputs + (list julia-colorvectorspace + julia-colors + julia-freetype + julia-geometrybasics)) + (home-page "https://github.com/JuliaGraphics/FreeTypeAbstraction.jl") + (synopsis "Julian abstraction layer over FreeType.jl") + (description + "This package provides an abstraction layer over the FreeType Julia module.") + (license license:expat))) + +;; ready to upstream +(define-public julia-observables + (package + (name "julia-observables") + (version "0.5.4") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/JuliaGizmos/Observables.jl") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1l0rk60nrwwgcifqs72x76z9dv1kq6rvcbhy63kp27yqfsx6c20s")))) + (build-system julia-build-system) + (home-page "https://github.com/JuliaGizmos/Observables.jl") + (synopsis "Observable ref") + (description "This package provides the @code{Observable}s type in Julia, +which are like @code{Ref}s but you can listen to changes.") + (license license:expat))) + (define-public julia-simplebufferstream (package (name "julia-simplebufferstream") @@ -1494,7 +2643,7 @@ that still support Julia versions older than 1.6.") ("julia-fileio" ,julia-fileio) ;("julia-imagefiltering" ,julia-imagefiltering) ("julia-imagemagick" ,julia-imagemagick) - ;("julia-quartzimageio" ,julia-quartzimageio) + ;("julia-quartzimageio" ,julia-quartzimageio) ; for macOS ("julia-requires" ,julia-requires))) ;(native-inputs ; `(;("julia-gtk" ,julia-gtk) diff --git a/gn/packages/maths.scm b/gn/packages/maths.scm index 1c1c1ae..7dfb896 100644 --- a/gn/packages/maths.scm +++ b/gn/packages/maths.scm @@ -3,6 +3,7 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix utils) + #:use-module (guix gexp) #:use-module (gnu packages gcc) #:use-module (gnu packages gperf) #:use-module (gnu packages maths) @@ -131,3 +132,110 @@ (inputs `(,@(fold alist-delete (package-inputs suitesparse) '("metis")))))) + +(define-public gsl-x86-64-v2 + (package/inherit gsl + (name "gsl-x86-64-v2") + (arguments + (substitute-keyword-arguments (package-arguments gsl) + ((#:make-flags flags #~'()) + #~(append (list "CFLAGS=-march=x86-64-v2" + "CXXFLAGS=-march=x86-64-v2") + #$flags)) + ((#:configure-flags flags #~'()) + #~(append (list (string-append "--libdir=" #$output + "/lib/glibc-hwcaps/x86-64-v2")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")) + (delete-file-recursively (string-append #$output "/include")))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t) + (tunable? . #f))))) + +(define-public gsl-x86-64-v3 + (package/inherit gsl + (name "gsl-x86-64-v3") + (arguments + (substitute-keyword-arguments (package-arguments gsl) + ((#:make-flags flags #~'()) + #~(append (list "CFLAGS=-march=x86-64-v3" + "CXXFLAGS=-march=x86-64-v3") + #$flags)) + ((#:configure-flags flags #~'()) + #~(append (list (string-append "--libdir=" #$output + "/lib/glibc-hwcaps/x86-64-v3")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")) + (delete-file-recursively (string-append #$output "/include")))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t) + (tunable? . #f))))) + +(define-public gsl-x86-64-v4 + (package/inherit gsl + (name "gsl-x86-64-v4") + (outputs '("out" "static")) + (arguments + (substitute-keyword-arguments (package-arguments gsl) + ((#:make-flags flags #~'()) + #~(append (list "CFLAGS=-march=x86-64-v4" + "CXXFLAGS=-march=x86-64-v4") + #$flags)) + ((#:configure-flags flags #~'()) + #~(append (list (string-append "--libdir=" #$output + "/lib/glibc-hwcaps/x86-64-v4")) + #$flags)) + ;; The building machine can't necessarily run the code produced. + ((#:tests? _ #t) #f) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'remove-extra-files + (lambda _ + (delete-file-recursively (string-append #$output "/bin")) + (delete-file-recursively (string-append #$output "/include")))))))) + (supported-systems '("x86_64-linux")) + (properties `((hidden? . #t) + (tunable? . #f))))) + +;; This copy of gsl will automatically use the libraries that target the +;; x86_64 psABI which the hardware supports. +(define-public gsl-hwcaps + (package/inherit gsl + (name "gsl-hwcaps") + (arguments + (substitute-keyword-arguments (package-arguments gsl) + ((#:phases phases #~%standard-phases) + #~(modify-phases #$phases + (add-after 'install 'install-optimized-libraries + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((hwcaps "/lib/glibc-hwcaps")) + (copy-recursively + (string-append (assoc-ref inputs "gsl-x86-64-v2") + hwcaps "/x86-64-v2") + (string-append #$output hwcaps "/x86-64-v2")) + (copy-recursively + (string-append (assoc-ref inputs "gsl-x86-64-v3") + hwcaps "/x86-64-v3") + (string-append #$output hwcaps "/x86-64-v3")) + (copy-recursively + (string-append (assoc-ref inputs "gsl-x86-64-v4") + hwcaps "/x86-64-v4") + (string-append #$output hwcaps "/x86-64-v4"))))))))) + (native-inputs + (modify-inputs (package-native-inputs gsl) + (append gsl-x86-64-v2 + gsl-x86-64-v3 + gsl-x86-64-v4))) + (properties `((tunable? . #f))))) diff --git a/gn/packages/ocaml.scm b/gn/packages/ocaml.scm index 4aa2543..7c6020a 100644 --- a/gn/packages/ocaml.scm +++ b/gn/packages/ocaml.scm @@ -1,9 +1,11 @@ (define-module (gn packages ocaml) #:use-module (guix packages) + #:use-module (guix download) #:use-module (guix git-download) #:use-module (guix build-system ocaml) #:use-module (gnu packages) - #:use-module (gnu packages ocaml)) + #:use-module (gnu packages ocaml) + #:use-module (gnu packages maths)) ;; This is the last version supported by ocaml-4.07. (define-public ocaml4.07-lwt-5.5.0 @@ -23,5 +25,26 @@ "1jbjz2rsz3j56k8vh5qlmm87hhkr250bs2m3dvpy9vsri8rkzj9z")))) (properties '())))) +(define-public ocaml4.07-gsl-1 + (package-with-ocaml4.07 + (package + (inherit ocaml-gsl) + (version "1.19.3") + (source (origin + (method url-fetch) + (uri (string-append "https://github.com/mmottl/gsl-ocaml" + "/releases/download/v" + version "/gsl-ocaml-" version ".tar.gz")) + (sha256 + (base32 + "0nzp43hp8pbjqkrxnwp5lgjrabxayf61h18fjaydi0s5faq6f3xh")))) + (build-system ocaml-build-system) + (inputs + `(("gsl" ,gsl-static))) + (native-inputs + `(("ocamlbuild" ,ocamlbuild))) + (arguments '()) + (propagated-inputs '())))) + (define-public build-with-ocaml4.07 (package-input-rewriting/spec `(("ocaml4.07-lwt" . ,(const ocaml4.07-lwt-5.5.0))))) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 510546d..e7cfdd7 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -3,6 +3,7 @@ #:use-module (gnu packages) #:use-module (gnu packages check) #:use-module (gnu packages compression) + #:use-module (gnu packages databases) #:use-module (gnu packages fontutils) #:use-module (gnu packages ghostscript) #:use-module (gnu packages icu4c) @@ -32,8 +33,10 @@ #:use-module (guix packages) #:use-module (guix download) #:use-module (guix git-download) + #:use-module (guix hg-download) #:use-module (guix gexp) #:use-module (guix utils) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (srfi srfi-1)) @@ -862,50 +865,6 @@ spreadsheets without the need for COM objects.") (description "Extensions to the standard Python datetime module") (license license:bsd-3))) -(define-public python-arvados-python-client - (package - (name "python-arvados-python-client") - (version "2.5.0") - (source - (origin - (method url-fetch) - (uri (pypi-uri "arvados-python-client" version)) - (sha256 - (base32 "1j08aykj0v2z2bqwr5nfnbjgc1yzdnfdafcnxbf2jbwqh8kx7zc9")) - (modules '((guix build utils))) - (snippet - '(begin - (substitute* "setup.py" - ;; Don't set a maximum version of pycurl. - (("(pycurl >=([[:digit:]]+\\.?)+),.*" _ pycurl) - (string-append pycurl "',\n"))))))) - (build-system python-build-system) - (arguments - `(#:tests? #f)) ; tests not included? - (propagated-inputs - (list python-ciso8601 - python-future - python-google-api-client - python-google-api-core-1 - python-google-auth-1 - python-httplib2 - python-protobuf - python-pycurl - python-pyparsing-2.4.7 ; < 3 - python-ruamel.yaml - python-ws4py)) - (native-inputs - (list python-mock - python-pbr-1.6.0 - python-pyyaml)) - (home-page "https://arvados.org") - (synopsis "Arvados client library") - (description "This package provides the arvados module, an API client for -Arvados. It also includes higher-level functions to help you write Crunch -scripts, and command-line tools to store and retrieve data in the Keep storage -server.") - (license license:asl2.0))) - (define-public python-pyshex (package (name "python-pyshex") @@ -1815,6 +1774,30 @@ file format spec.") (license:fsf-free (string-append "https://web.archive.org/web/20190211105114/" "http://www.repoze.org/LICENSE.txt"))))) +;; Note: This package is only needed for rdflib < 6.0; supersede when +;; the above are removed. +(define-public python-rdflib-jsonld + (package + (name "python-rdflib-jsonld") + (version "0.6.2") + (source + (origin + (method url-fetch) + (uri (pypi-uri "rdflib-jsonld" version)) + (sha256 + (base32 + "0qrshlqzv5g5bign7kjja3xf7hyk7xgayr3yd0qlqda1kl0x6z0h")))) + (build-system python-build-system) + (native-inputs + (list python-nose)) + (propagated-inputs + (list python-rdflib)) + (home-page "https://github.com/RDFLib/rdflib-jsonld") + (synopsis "rdflib extension adding JSON-LD parser and serializer") + (description "This package provides an rdflib extension adding JSON-LD +parser and serializer.") + (license license:bsd-3))) + (define-public python-rdflib-shim (package (name "python-rdflib-shim") @@ -1878,3 +1861,97 @@ complete wrapping of the HDF5 API, while the high-level component supports access to HDF5 files, datasets and groups using established Python and NumPy concepts.") (license license:bsd-3))) + +(define-public python-typing-extensions-4.10 + (package + (inherit python-typing-extensions) + (version "4.10.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "typing_extensions" version)) + (sha256 + (base32 + "1jxkj4pni8pdyrn79sq441lsp40xzw363n0qvfc6zfcgkv4dgaxh")))))) + +(define-public python-addict + (package + (name "python-addict") + (version "2.4.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "addict" version)) + (sha256 + (base32 + "1574sicy5ydx9pvva3lbx8qp56z9jbdwbj26aqgjhyh61q723cmk")))) + (build-system pyproject-build-system) + (home-page "https://github.com/mewwts/addict") + (synopsis "Python dictionary with attribute accessible values") + (description "@code{python-addict} provides dictionaries whose items can +be get and set using both attribute and item syntax.") + (license license:expat))) + +(define-public python-enlighten + (package + (name "python-enlighten") + (version "1.12.4") + (source (origin + (method url-fetch) + (uri (pypi-uri "enlighten" version)) + (sha256 + (base32 + "0psvglhi0c7d7pdk9rfb8scnv3xbq2fz78619x2mxvz094mxkwvm")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-blessed python-prefixed)) + (home-page "https://github.com/Rockhopper-Technologies/enlighten") + (synopsis "Console progress bar library") + (description "@code{python-enlighten} is a console progress bar library +for Python. The main advantage of Enlighten is that it allows writing to +stdout and stderr without any redirection or additional code---just print or +log as you normally would. Enlighten also includes experimental support for +Jupyter Notebooks.") + (license license:mpl2.0))) + +(define-public python-pypubsub + (package + (name "python-pypubsub") + (version "4.0.3") + ;; There is no source tarball on PyPI. + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/schollii/pypubsub") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "02j74w28wzmdvxkk8i561ywjgizjifq3hgcl080yj0rvkd3wivlb")))) + (build-system python-build-system) + (home-page "https://github.com/schollii/pypubsub") + (synopsis "Python publish-subscribe library") + (description "@code{python-pypubsub} provides a pure Python +publish-subscribe API to facilitate event-based or message-based architecture +in a single-process application. It is centered on the notion of a topic; +senders publish messages of a given topic, and listeners subscribe to messages +of a given topic, all inside the same process. The package also supports a +variety of advanced features that facilitate debugging and maintaining topics +and messages in larger desktop or server-based applications.") + (license license:bsd-2))) + +(define-public python-prefixed + (package + (name "python-prefixed") + (version "0.7.0") + (source (origin + (method url-fetch) + (uri (pypi-uri "prefixed" version)) + (sha256 + (base32 + "1sdvxwy4kvcxvnq1nx70j1ccx5ga6wdb478vqd5azf1fc1gd2m0b")))) + (build-system pyproject-build-system) + (home-page "https://github.com/Rockhopper-Technologies/prefixed") + (synopsis "Prefixed alternative numeric library") + (description "@code{python-prefixed} provides an alternative +implementation of the built-in float which supports formatted output with +SI (decimal) and IEC (binary) prefixes.") + (license license:mpl2.0))) diff --git a/gn/packages/ratspub.scm b/gn/packages/ratspub.scm index 726bc0b..19b70c2 100644 --- a/gn/packages/ratspub.scm +++ b/gn/packages/ratspub.scm @@ -179,6 +179,20 @@ gene-keyword relationships are presented as an interactive graph and a table.") `(modify-phases ,phases (delete 'check)))))))) +(define-public python-keras-no-tests + (hidden-package + (package + (inherit python-keras) + (source + (origin + (inherit (package-source python-keras)))) + (arguments + (substitute-keyword-arguments (package-arguments python-keras) + ((#:phases phases) + `(modify-phases ,phases + (delete 'check)))))))) + + (define-public hrdp-project (package (name "hrdp-project") @@ -370,7 +384,7 @@ if __name__ == '__main__': ("inetutils" ,inetutils) ("python-bcrypt" ,python-bcrypt) ("python-flask-sqlalchemy" ,python-flask-sqlalchemy) - ("python-keras" ,python-keras-for-ratspub) + ("python-keras" ,python-keras-no-tests) ("python-nltk" ,python-nltk) ("python-pandas" ,python-pandas) ("python-regex" ,python-regex) diff --git a/gn/packages/riscv.scm b/gn/packages/riscv.scm index ae4a72e..e87f8a9 100644 --- a/gn/packages/riscv.scm +++ b/gn/packages/riscv.scm @@ -13,7 +13,6 @@ #:use-module (gn packages fpga) #:use-module (gnu packages cpp) #:use-module (gnu packages virtualization) - #:use-module (guix build utils) #:use-module (guix build-system gnu) #:use-module (guix gexp) #:use-module (guix git-download) diff --git a/gn/packages/ruby.scm b/gn/packages/ruby.scm index e2c4164..befb550 100644 --- a/gn/packages/ruby.scm +++ b/gn/packages/ruby.scm @@ -5983,13 +5983,17 @@ Simple gem that adds various color methods to String class, and can be used as f (base32 "0yzlf56ynj545ln5dxl422rpi8r6h11cr6rag5hk2qpbkzs6l9c2")))) (build-system ruby-build-system) + (inputs + (list lmdb)) (native-inputs `(("ruby-rake" ,ruby-rake) ("ruby-rake-compiler" ,ruby-rake-compiler) - ("ruby-rspec" ,ruby-rspec) ("ruby-rspec" ,ruby-rspec))) + ("ruby-rspec" ,ruby-rspec) + ("ruby-ruby-memcheck" ,ruby-ruby-memcheck) + )) (arguments - `(#:tests? #f ; There are no tests. - )) (synopsis "lmdb is a Ruby binding to OpenLDAP Lightning MDB.") + `(#:tests? #f)) + (synopsis "lmdb is a Ruby binding to OpenLDAP Lightning MDB.") (description "lmdb is a Ruby binding to OpenLDAP Lightning MDB.") (home-page "https://github.com/doriantaylor/rb-lmdb") (license license:expat))) diff --git a/gn/packages/virtualization.scm b/gn/packages/virtualization.scm index 9e7efd7..e0eb016 100644 --- a/gn/packages/virtualization.scm +++ b/gn/packages/virtualization.scm @@ -21,7 +21,7 @@ (define-public gem5 (package (name "gem5") - (version "21.2.1.0") + (version "22.1.0.0") (source (origin (method git-fetch) @@ -30,7 +30,7 @@ (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 - (base32 "0wyns8cfkigzw3m21331m8ydc7akm8l2lp0kci4pq8jyzsanmjm3")) + (base32 "1kcdn8rawzhf88lcb2app8m1r1px4ba041kyl7xigslix7qs05k3")) (snippet #~(begin (use-modules (guix build utils)) @@ -38,6 +38,7 @@ (substitute* "src/base/date.cc" (("__DATE__") "\"1970-01-01\"") (("__TIME__") "\"00:00:00\"")) + ;; Remove vendored pybind11. (substitute* "ext/sst/Makefile" (("-I../../ext/pybind11/include/") "${shell pybind11-config --includes}")) diff --git a/gn/services/bh20-seq-resource-container.scm b/gn/services/bh20-seq-resource-container.scm deleted file mode 100644 index e0eccf7..0000000 --- a/gn/services/bh20-seq-resource-container.scm +++ /dev/null @@ -1,110 +0,0 @@ -(define-module (gn services bh20-seq-resource-container)) - -(use-modules (gnu) - (gn packages bioinformatics) - (guix modules) - ((guix packages) #:select (package-source)) - (guix records) - (guix build-system python) ; for python-version from guix/build/python-build-system.scm - (ice-9 match)) -(use-service-modules shepherd) -(use-package-modules compression python python-web) - -(define-record-type* <covid19-pubseq-configuration> - covid19-pubseq-configuration - make-covid19-pubseq-configuration - covid19-pubseq-configuration? - (package covid19-pubseq-configuration-package ; package - (default bh20-seq-resource-for-service)) - (deploy-directory covid19-pubseq-deploy-directory ; string - (default "/srv/http")) - (port covid19-pubseq-configuration-port ; string - (default "5000"))) - -(define covid19-pubseq-activation-service - (match-lambda - (($ <covid19-pubseq-configuration> package deploy-directory port) - #~(begin - (let ((pkg-src #$(package-source package))) - (when (file-exists? #$deploy-directory) - (delete-file-recursively (mkdir-p #$deploy-directory))) - (mkdir-p #$deploy-directory) - (if (file-is-directory? pkg-src) - (copy-recursively pkg-src #$deploy-directory) - (begin - (copy-file pkg-src #$(string-append deploy-directory - "/src.tar.xz")) - (with-directory-excursion #$deploy-directory - (invoke #$(file-append xz "/bin/xz") "-d" "src.tar.xz") - (invoke #$(file-append tar "/bin/tar") "xvf" "src.tar" - "--strip-components=1"))))))))) - -(define covid19-pubseq-shepherd-service - (match-lambda - (($ <covid19-pubseq-configuration> package deploy-directory port) - (with-imported-modules (source-module-closure - '((gnu build shepherd) - (gnu system file-systems))) - (list (shepherd-service - (provision '(covid19-pubseq)) - (requirement '(networking)) - (modules '((gnu build shepherd) - (gnu system file-systems))) - ;(start #~(make-forkexec-constructor/container - (start #~(make-forkexec-constructor - (list - #$(file-append gunicorn "/bin/gunicorn") - (string-append "-blocalhost:" #$port) - "bh20simplewebuploader.main:app") - #:directory #$deploy-directory - #:log-file "/var/log/covid19-pubseq.log" - #:environment-variables - ;(let (pyversion (python-version (@ (gnu packages python) python))) - '("TMPDIR=/export/tmp" - "PYTHONPATH=/run/current-system/profile/lib/python3.9/site-packages") - ; (string-append "PYTHONPATH=/run/current-system/profile/lib/python" pyversion "/site-packages"))) - ;#:mappings - ;(list (file-system-mapping - ; (source "/export/tmp") - ; (target source) - ; (writable? #t)) - ; (file-system-mapping - ; ;; TODO: Don't hardcode python version! - ; (source "/run/current-system/profile/lib/python3.9/site-packages") - ; (target source))) - )) - (stop #~(make-kill-destructor)))))))) - -(define covid19-pubseq-service-type - (service-type - (name 'covid19-pubseq) - (extensions - (list - (service-extension shepherd-root-service-type - covid19-pubseq-shepherd-service) - (service-extension activation-service-type - covid19-pubseq-activation-service) - (service-extension profile-service-type - (compose list - covid19-pubseq-configuration-package)))) - (default-value (covid19-pubseq-configuration)) - (description - "Run a COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource Webserver."))) - -(operating-system - (host-name "covid19-pubseq") - (timezone "Etc/UTC") - (locale "en_US.utf8") - - (bootloader (bootloader-configuration - (bootloader grub-bootloader) - (targets '("does-not-matter")))) - (file-systems %base-file-systems) - ;; No firmware for VMs. - (firmware '()) - ;; We don't need any packages inside the container. - (packages '()) - - (services (list (service covid19-pubseq-service-type)))) - -;; guix system container /home/shepherd/guix-bioinformatics/gn/services/bh20-seq-resource-container.scm --share=/export/tmp=/export/tmp --network diff --git a/gn/services/pluto.scm b/gn/services/pluto.scm index 720b769..420e2cf 100644 --- a/gn/services/pluto.scm +++ b/gn/services/pluto.scm @@ -43,21 +43,14 @@ (requirement '(networking)) (modules '((gnu build shepherd) (gnu system file-systems))) - (start #~(make-forkexec-constructor/container - ;(list #$(file-append package "/runpluto.sh") #$port) - (list #$(file-append package "/runpluto")) + (start #~(make-forkexec-constructor + '(#$(file-append package "/bin/runsliderserver")) #:log-file "/var/log/pluto.log" #:user "julia" #:group "julia" - ;; This prevents the service from using /root as $HOME. - #:environment-variables '() - #:mappings (list (file-system-mapping - (source "/home/jovyan") - (target source) - (writable? #t)) - (file-system-mapping - (source "/etc/ssl") - (target source))))) + #:environment-variables + (list "SSL_CERT_DIR=/etc/ssl/certs" + "SSL_CERT_FILE=/etc/ssl/certs/ca-certificates.crt"))) (stop #~(make-kill-destructor)))))))) (define pluto-service-type diff --git a/lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch b/lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch new file mode 100644 index 0000000..55036a7 --- /dev/null +++ b/lizardfs-issues-found-on-Fedora-34-using-GCC-11.patch @@ -0,0 +1,111 @@ +From 1da538a07974b8b1afd2580af2828418cbdad42b Mon Sep 17 00:00:00 2001 +Message-ID: <1da538a07974b8b1afd2580af2828418cbdad42b.1699426938.git.efraim@flashner.co.il> +From: Marcin Konarski <marcin.konarski@lizardfs.com> +Date: Fri, 21 May 2021 12:36:56 +0200 +Subject: [PATCH] all: Fix build issues found on Fedora 34 using GCC 11.1.1 + +Change-Id: I1c20e914d249d367d0a058de1102ae62dcaf6054 +--- + src/common/ec_read_plan.h | 2 +- + src/common/flat_set_unittest.cc | 4 ++-- + src/common/vector_range.h | 1 + + src/data/CMakeLists.txt | 25 +++++++++++++++++++++++ + src/master/goal_config_loader_unittest.cc | 4 ++-- + 5 files changed, 31 insertions(+), 5 deletions(-) + +diff --git a/src/common/ec_read_plan.h b/src/common/ec_read_plan.h +index c96413cb..bda10cb5 100644 +--- a/src/common/ec_read_plan.h ++++ b/src/common/ec_read_plan.h +@@ -132,7 +132,7 @@ protected: + } + } + +- for (const auto op : read_operations) { ++ for (auto const& op : read_operations) { + data_parts[op.first.getSlicePart()] = buffer + op.second.buffer_offset; + } + +diff --git a/src/common/flat_set_unittest.cc b/src/common/flat_set_unittest.cc +index 9ad760c4..e50308eb 100644 +--- a/src/common/flat_set_unittest.cc ++++ b/src/common/flat_set_unittest.cc +@@ -62,9 +62,9 @@ TEST(FlatSet, RedundantInsert) { + // const & + std::initializer_list<std::string> elems2 = {"0", "1", "2", "3", "4"}; + flat_set<std::string> cs2(elems2); +- for (const std::string &i : {"2", "4"}) { ++ for (char const* s : {"2", "4"}) { + EXPECT_EQ(cs2.size(), elems2.size()); +- cs2.insert(i); ++ cs2.insert(s); + EXPECT_EQ(cs2.size(), elems2.size()); + } + } +diff --git a/src/common/vector_range.h b/src/common/vector_range.h +index f336e1ec..57bba8dd 100644 +--- a/src/common/vector_range.h ++++ b/src/common/vector_range.h +@@ -22,6 +22,7 @@ + + #include <algorithm> + #include <cassert> ++#include <limits> + #include <stdexcept> + + /*! \brief Class providing std::vector like interface to subrange of vector. */ +diff --git a/src/data/CMakeLists.txt b/src/data/CMakeLists.txt +index 88c20d5d..bf69a5e2 100644 +--- a/src/data/CMakeLists.txt ++++ b/src/data/CMakeLists.txt +@@ -16,3 +16,28 @@ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/mfschunkserver.cfg DESTINATION ${ETC_S + install(FILES ${CMAKE_CURRENT_BINARY_DIR}/mfsmetalogger.cfg DESTINATION ${ETC_SUBDIR} RENAME mfsmetalogger.cfg.dist) + + install(FILES lizardfs.completion DESTINATION etc/bash_completion.d RENAME lizardfs) ++ ++if(BUILD_TESTS) ++ # Create a mock include dir. ++ # We do this because we want to preserve the proper include directives in the example code ++ # and still build this example program in the build step before the needed headers are installed. ++ file(MAKE_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}/include/lizardfs) ++ add_custom_command( ++ OUTPUT ++ ${CMAKE_CURRENT_BINARY_DIR}/include/lizardfs/lizardfs_c_api.h ++ ${CMAKE_CURRENT_BINARY_DIR}/include/lizardfs/lizardfs_error_codes.h ++ COMMAND ${CMAKE_COMMAND} -E create_symlink ++ ${CMAKE_SOURCE_DIR}/src/mount/client/lizardfs_c_api.h ++ ${CMAKE_CURRENT_BINARY_DIR}/include/lizardfs/lizardfs_c_api.h ++ COMMAND ${CMAKE_COMMAND} -E create_symlink ++ ${CMAKE_SOURCE_DIR}/src/common/lizardfs_error_codes.h ++ ${CMAKE_CURRENT_BINARY_DIR}/include/lizardfs/lizardfs_error_codes.h ++ ) ++ add_executable(c-client-example ++ liblizardfs-client-example.c ++ ${CMAKE_CURRENT_BINARY_DIR}/include/lizardfs/lizardfs_c_api.h ++ ${CMAKE_CURRENT_BINARY_DIR}/include/lizardfs/lizardfs_error_codes.h) ++ target_include_directories(c-client-example PRIVATE ${CMAKE_CURRENT_BINARY_DIR}/include) ++ target_link_libraries(c-client-example lizardfs-client stdc++) ++ install(TARGETS c-client-example RUNTIME DESTINATION ${BIN_SUBDIR}) ++endif() +diff --git a/src/master/goal_config_loader_unittest.cc b/src/master/goal_config_loader_unittest.cc +index 050e8a52..a236dba9 100644 +--- a/src/master/goal_config_loader_unittest.cc ++++ b/src/master/goal_config_loader_unittest.cc +@@ -41,8 +41,8 @@ Goal::Slice createSlice(int type, + std::vector<std::map<std::string, int>> part_list) { + Goal::Slice slice{Goal::Slice::Type(type)}; + int part_index = 0; +- for (const auto &part : part_list) { +- for (const auto label : part) { ++ for (auto const& part : part_list) { ++ for (auto const& label : part) { + slice[part_index][MediaLabel(label.first)] += label.second; + } + ++part_index; + +base-commit: 6f6fd530f8fa286fbfb6a050cacbba73e928bd26 +-- +Efraim Flashner <efraim@flashner.co.il> רנשלפ םירפא +GPG key = A28B F40C 3E55 1372 662D 14F7 41AA E7DC CA3D 8351 +Confidentiality cannot be guaranteed on emails sent or received unencrypted + diff --git a/seqwish-paryfor-riscv.diff b/seqwish-paryfor-riscv.diff new file mode 100644 index 0000000..cecf806 --- /dev/null +++ b/seqwish-paryfor-riscv.diff @@ -0,0 +1,20 @@ +diff --git a/deps/paryfor/paryfor.hpp b/deps/paryfor/paryfor.hpp +index b8ced09..0536580 100644 +--- a/deps/paryfor/paryfor.hpp ++++ b/deps/paryfor/paryfor.hpp +@@ -51,6 +51,15 @@ static inline void spin_loop_pause() noexcept { + } + } // namespace atomic_queue + } // namespace paryfor ++#elif defined(__riscv) && (__riscv_xlen == 64) ++namespace paryfor { ++namespace atomic_queue { ++constexpr int CACHE_LINE_SIZE = 64; ++static inline void spin_loop_pause() noexcept { ++ asm volatile ("nop" ::: "memory"); ++} ++} ++} + #else + #error "Unknown CPU architecture." + #endif diff --git a/seqwish-shared-library.diff b/seqwish-shared-library.diff new file mode 100644 index 0000000..be982de --- /dev/null +++ b/seqwish-shared-library.diff @@ -0,0 +1,195 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 09eafb5..a39f90f 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -7,6 +7,8 @@ project(seqwish) + # We build using c++14 + set(CMAKE_CXX_STANDARD 14) + ++include(GNUInstallDirs) ++ + set(THREADS_PREFER_PTHREAD_FLAG ON) + find_package(Threads REQUIRED) + +@@ -26,6 +28,8 @@ if(NOT DEFINED EXTRA_FLAGS) + "Extra compilation flags for C and CXX." FORCE) + endif() + ++set(SEQWISH_LINK_SHARED_LIBRARY OFF CACHE BOOL "Do not link against the libseqwish shared library") ++ + if (${CMAKE_BUILD_TYPE} MATCHES Release) + set(EXTRA_FLAGS "-Ofast ${EXTRA_FLAGS}") + set(CMAKE_CXX_FLAGS_RELEASE "-DNDEBUG") # reset CXX_FLAGS to replace -O3 with -Ofast +@@ -82,7 +86,7 @@ include(${CMAKE_ROOT}/Modules/ExternalProject.cmake) + # sdsl-lite (full build using its cmake config) + ExternalProject_Add(sdsl-lite + SOURCE_DIR "${CMAKE_SOURCE_DIR}/deps/sdsl-lite" +- CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>" ++ CMAKE_ARGS "${CMAKE_ARGS};-DCMAKE_CXX_FLAGS=-fPIC;-DCMAKE_C_FLAGS=-fPIC;-DCMAKE_INSTALL_PREFIX=<INSTALL_DIR>" + UPDATE_COMMAND "" + INSTALL_COMMAND "") + ExternalProject_Get_property(sdsl-lite INSTALL_DIR) +@@ -203,27 +207,125 @@ set(mio_INCLUDE "${SOURCE_DIR}/include") + #set(CMAKE_BUILD_TYPE Debug) + set(CMAKE_BUILD_TYPE Release) + ++# set up our target libraries and specify its dependencies and includes ++add_library( libseqwish_static ++ ${CMAKE_SOURCE_DIR}/src/utils.cpp ++ ${CMAKE_SOURCE_DIR}/src/tempfile.cpp ++ ${CMAKE_SOURCE_DIR}/src/main.cpp ++ ${CMAKE_SOURCE_DIR}/src/seqindex.cpp ++ ${CMAKE_SOURCE_DIR}/src/paf.cpp ++ ${CMAKE_SOURCE_DIR}/src/sxs.cpp ++ ${CMAKE_SOURCE_DIR}/src/cigar.cpp ++ ${CMAKE_SOURCE_DIR}/src/alignments.cpp ++ ${CMAKE_SOURCE_DIR}/src/pos.cpp ++ ${CMAKE_SOURCE_DIR}/src/match.cpp ++ ${CMAKE_SOURCE_DIR}/src/transclosure.cpp ++ ${CMAKE_SOURCE_DIR}/src/links.cpp ++ ${CMAKE_SOURCE_DIR}/src/compact.cpp ++ ${CMAKE_SOURCE_DIR}/src/dna.cpp ++ ${CMAKE_SOURCE_DIR}/src/gfa.cpp ++ ${CMAKE_SOURCE_DIR}/src/vgp.cpp ++ ${CMAKE_SOURCE_DIR}/src/exists.cpp ++ ${CMAKE_SOURCE_DIR}/src/time.cpp ++ ${CMAKE_SOURCE_DIR}/src/mmap.cpp ++ ) ++add_dependencies(libseqwish_static tayweeargs) ++add_dependencies(libseqwish_static sdsl-lite) ++add_dependencies(libseqwish_static gzipreader) ++add_dependencies(libseqwish_static mmmulti) ++add_dependencies(libseqwish_static iitii) ++add_dependencies(libseqwish_static ips4o) ++add_dependencies(libseqwish_static bbhash) ++add_dependencies(libseqwish_static atomicbitvector) ++add_dependencies(libseqwish_static atomicqueue) ++add_dependencies(libseqwish_static ska) ++add_dependencies(libseqwish_static paryfor) ++add_dependencies(libseqwish_static mio) ++target_include_directories(libseqwish_static PUBLIC ++ "${sdsl-lite_INCLUDE}" ++ "${sdsl-lite-divsufsort_INCLUDE}" ++ "${tayweeargs_INCLUDE}" ++ "${gzipreader_INCLUDE}" ++ "${ips4o_INCLUDE}" ++ "${mmmulti_INCLUDE}" ++ "${iitii_INCLUDE}" ++ "${bbhash_INCLUDE}" ++ "${atomicbitvector_INCLUDE}" ++ "${atomicqueue_INCLUDE}" ++ "${ska_INCLUDE}" ++ "${paryfor_INCLUDE}" ++ "${mio_INCLUDE}") ++target_link_libraries(libseqwish_static ++ "${sdsl-lite_LIB}/libsdsl.a" ++ "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" ++ "${sdsl-lite-divsufsort_LIB}/libdivsufsort64.a" ++ "-latomic" ++ Threads::Threads ++ jemalloc ++ z) ++set_target_properties(libseqwish_static PROPERTIES OUTPUT_NAME "seqwish") ++ ++add_library( libseqwish SHARED ++ ${CMAKE_SOURCE_DIR}/src/utils.cpp ++ ${CMAKE_SOURCE_DIR}/src/tempfile.cpp ++ ${CMAKE_SOURCE_DIR}/src/main.cpp ++ ${CMAKE_SOURCE_DIR}/src/seqindex.cpp ++ ${CMAKE_SOURCE_DIR}/src/paf.cpp ++ ${CMAKE_SOURCE_DIR}/src/sxs.cpp ++ ${CMAKE_SOURCE_DIR}/src/cigar.cpp ++ ${CMAKE_SOURCE_DIR}/src/alignments.cpp ++ ${CMAKE_SOURCE_DIR}/src/pos.cpp ++ ${CMAKE_SOURCE_DIR}/src/match.cpp ++ ${CMAKE_SOURCE_DIR}/src/transclosure.cpp ++ ${CMAKE_SOURCE_DIR}/src/links.cpp ++ ${CMAKE_SOURCE_DIR}/src/compact.cpp ++ ${CMAKE_SOURCE_DIR}/src/dna.cpp ++ ${CMAKE_SOURCE_DIR}/src/gfa.cpp ++ ${CMAKE_SOURCE_DIR}/src/vgp.cpp ++ ${CMAKE_SOURCE_DIR}/src/exists.cpp ++ ${CMAKE_SOURCE_DIR}/src/time.cpp ++ ${CMAKE_SOURCE_DIR}/src/mmap.cpp ++ ${CMAKE_SOURCE_DIR}/src/version.cpp ++ ) ++add_dependencies(libseqwish tayweeargs) ++add_dependencies(libseqwish sdsl-lite) ++add_dependencies(libseqwish gzipreader) ++add_dependencies(libseqwish mmmulti) ++add_dependencies(libseqwish iitii) ++add_dependencies(libseqwish ips4o) ++add_dependencies(libseqwish bbhash) ++add_dependencies(libseqwish atomicbitvector) ++add_dependencies(libseqwish atomicqueue) ++add_dependencies(libseqwish ska) ++add_dependencies(libseqwish paryfor) ++add_dependencies(libseqwish mio) ++target_include_directories(libseqwish PUBLIC ++ "${sdsl-lite_INCLUDE}" ++ "${sdsl-lite-divsufsort_INCLUDE}" ++ "${tayweeargs_INCLUDE}" ++ "${gzipreader_INCLUDE}" ++ "${ips4o_INCLUDE}" ++ "${mmmulti_INCLUDE}" ++ "${iitii_INCLUDE}" ++ "${bbhash_INCLUDE}" ++ "${atomicbitvector_INCLUDE}" ++ "${atomicqueue_INCLUDE}" ++ "${ska_INCLUDE}" ++ "${paryfor_INCLUDE}" ++ "${mio_INCLUDE}") ++target_link_libraries(libseqwish ++ "${sdsl-lite_LIB}/libsdsl.a" ++ "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" ++ "${sdsl-lite-divsufsort_LIB}/libdivsufsort64.a" ++ "-latomic" ++ Threads::Threads ++ jemalloc ++ z) ++set_target_properties(libseqwish PROPERTIES OUTPUT_NAME "seqwish") ++ + # set up our target executable and specify its dependencies and includes + add_executable(seqwish +- ${CMAKE_SOURCE_DIR}/src/utils.cpp +- ${CMAKE_SOURCE_DIR}/src/tempfile.cpp + ${CMAKE_SOURCE_DIR}/src/main.cpp +- ${CMAKE_SOURCE_DIR}/src/seqindex.cpp +- ${CMAKE_SOURCE_DIR}/src/paf.cpp +- ${CMAKE_SOURCE_DIR}/src/sxs.cpp +- ${CMAKE_SOURCE_DIR}/src/cigar.cpp +- ${CMAKE_SOURCE_DIR}/src/alignments.cpp +- ${CMAKE_SOURCE_DIR}/src/pos.cpp +- ${CMAKE_SOURCE_DIR}/src/match.cpp +- ${CMAKE_SOURCE_DIR}/src/transclosure.cpp +- ${CMAKE_SOURCE_DIR}/src/links.cpp +- ${CMAKE_SOURCE_DIR}/src/compact.cpp +- ${CMAKE_SOURCE_DIR}/src/dna.cpp +- ${CMAKE_SOURCE_DIR}/src/gfa.cpp +- ${CMAKE_SOURCE_DIR}/src/vgp.cpp +- ${CMAKE_SOURCE_DIR}/src/exists.cpp +- ${CMAKE_SOURCE_DIR}/src/time.cpp +- ${CMAKE_SOURCE_DIR}/src/mmap.cpp + ${CMAKE_SOURCE_DIR}/src/version.cpp + ) + add_dependencies(seqwish tayweeargs) +@@ -252,6 +354,11 @@ target_include_directories(seqwish PUBLIC + "${ska_INCLUDE}" + "${paryfor_INCLUDE}" + "${mio_INCLUDE}") ++if( SEQWISH_LINK_SHARED_LIBRARY ) ++ target_link_libraries( seqwish libseqwish ) ++else() ++ target_link_libraries( seqwish libseqwish_static ) ++endif() + target_link_libraries(seqwish + "${sdsl-lite_LIB}/libsdsl.a" + "${sdsl-lite-divsufsort_LIB}/libdivsufsort.a" +@@ -269,4 +376,6 @@ endif() + file(MAKE_DIRECTORY ${CMAKE_SOURCE_DIR}/include) + execute_process(COMMAND bash ${CMAKE_SOURCE_DIR}/scripts/generate_git_version.sh ${CMAKE_SOURCE_DIR}/include) + +-install(TARGETS seqwish DESTINATION bin) ++install(TARGETS seqwish DESTINATION "${CMAKE_INSTALL_BIDIR}") ++install(TARGETS libseqwish LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}") ++install(TARGETS libseqwish_static ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}") |