diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 444 |
1 files changed, 402 insertions, 42 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 2d1b55f..db420b7 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -23,7 +23,6 @@ #:use-module (gn packages java) #:use-module (gn packages ocaml) #:use-module (gn packages python) - #:use-module (gn packages twint) #:use-module (gnu packages algebra) #:use-module (gnu packages assembly) #:use-module (gnu packages autotools) @@ -33,6 +32,7 @@ #:use-module (gnu packages bioinformatics) #:use-module (gnu packages boost) #:use-module (gnu packages bootstrap) + #:use-module (gnu packages c) #:use-module (gnu packages check) #:use-module (gnu packages cmake) #:use-module (gnu packages compression) @@ -54,6 +54,7 @@ #:use-module (gnu packages java) #:use-module (gnu packages jemalloc) #:use-module (gnu packages linux) + #:use-module (gnu packages llvm) #:use-module (gnu packages machine-learning) #:use-module (gnu packages maths) #:use-module (gnu packages mpi) @@ -460,7 +461,7 @@ reads.") (description "Variant detection in massively parallel sequencing data.") ;; Free for non-commercial use by academic, government, and ;; non-profit/not-for-profit institutions - (license license:non-copyleft))) + (license (license:non-copyleft "file:///LICENSE")))) (define-public edirect-gn (deprecated-package "edirect-gn" edirect)) @@ -487,7 +488,7 @@ reads.") (arguments `(#:install-source? #f #:cargo-inputs - (("rust-clap" ,rust-clap-3.1) + (("rust-clap" ,rust-clap-3) ("rust-rustc-hash" ,rust-rustc-hash-1) ("rust-regex" ,rust-regex-1) ("rust-handlegraph" ,rust-handlegraph-0.7) @@ -510,6 +511,305 @@ reads.") collapses them into a non-redundant graph structure.") (license license:expat))) +(define-public gafpack + (let ((commit "ad31875b6914d964c6fd72d1bf334f0843538fb6") ; November 10, 2022 + (revision "1")) + (package + (name "gafpack") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/gafpack") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0di2psh0ls7jlbnqs7k71p55f73pn23a09k1h3ril7gwjcrzr3rk")))) + (build-system cargo-build-system) + (arguments + `(#:install-source? #f + #:cargo-inputs + (("rust-clap" ,rust-clap-4) + ("rust-gfa" ,rust-gfa-0.10)))) + (home-page "https://github.com/ekg/gafpack") + (synopsis "Convert variation graph alignments to coverage maps over nodes") + (description + "Gafpack converts alignments to pangenome variation graphs to coverage +maps useful in haplotype-based genotyping.") + (license license:expat)))) + +(define-public agc-for-pgr-tk + (let ((commit "453c0afdc54b4aa00fa8e97a63f196931fdb81c4") ; April 26, 2022 + (revision "1")) + (package + (name "agc") + (version (git-version "2.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/cschin/agc") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1v5s79rl38dcyy5h1lykbp6clcbqq9winn533j54y49q1jp8chix")) + (snippet + #~(begin + (use-modules (guix build utils)) + ;; Copy the two radul files we can't find a replacement for: + ;; https://github.com/refresh-bio/RADULS + (mkdir "keep-libs") + (rename-file "libs/raduls.h" "keep-libs/raduls.h") + (rename-file "libs/libraduls.a" "keep-libs/libraduls.a") + (delete-file-recursively "libs") + (rename-file "keep-libs" "libs") + + (delete-file-recursively "py_agc_api/pybind11-2.8.1") + (substitute* '("makefile" "makefile.release") + (("-mavx") "") + (("-m64") "") + (("\\$\\(AGC_LIBS_DIR)\\/mimalloc/\\$\\(LIB_ALLOC\\)") + "$(pkg-config --cflags --libs mimalloc) /usr/lib/libmimalloc.so") + (("\\$\\(AGC_LIBS_DIR)\\/\\$\\(LIB_ZLIB\\)") + "$(pkg-config --cflags --libs zlib) /usr/lib/libz.so") + (("\\$\\(AGC_LIBS_DIR)\\/\\$\\(LIB_ZSTD\\)") + "$(pkg-config --cflags --libs libzstd) /usr/lib/libzstd.so") + (("^PYBIND11_LIB = .*") "PYBIND11_LIB = /usr/include/pybind11") + (("\\$\\(PYBIND11_LIB\\)/include") "$(PYBIND11_LIB)")) + (substitute* (find-files "src" "\\.(h|cpp)$") + (("../../libs/ketopt.h") "ketopt.h") + (("../../libs/zlib.h") "zlib.h") + (("../../libs/zstd.h") "zstd.h")))))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; No tests. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; No configure script. + (add-after 'unpack 'adjust-sources + (lambda* (#:key inputs #:allow-other-keys) + (let ((mimalloc (assoc-ref inputs "mimalloc"))) + (substitute* '("makefile" "makefile.release") + (("/usr/include/pybind11") + (search-input-directory inputs "/include/pybind11")) + (("/usr/lib/libmimalloc.so") + (search-input-file inputs "/lib/libmimalloc.so")) + (("/usr/lib/libz.so") + (search-input-file inputs "/lib/libz.so")) + (("/usr/lib/libzstd.so") + (search-input-file inputs "/lib/libzstd.so")) + (("pkg-config") ,(pkg-config-for-target)))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (include (string-append out "/include/"))) + (install-file "agc" (string-append out "/bin")) + (install-file "libagc.so" (string-append out "/lib")) + (mkdir-p (string-append include "app")) + (mkdir-p (string-append include "core")) + (mkdir-p (string-append include "lib-cxx")) + (with-directory-excursion "src" + (for-each + (lambda (file) + (copy-file file (string-append include file))) + (find-files "." "\\.h$"))))))))) + (native-inputs + (list minimap2 ; for ketopt.h + pkg-config)) + (inputs + (list mimalloc + python + pybind11 + zlib + (list zstd "lib"))) + (home-page "https://github.com/cschin/agc") + (synopsis "Assembled Genomes Compressor") + (description + "@acronym{Assembled Genomes Compressor, AGC} is a tool designed to +compress collections of de-novo assembled genomes. It can be used for various +types of datasets: short genomes (viruses) as well as long (humans).") + (license license:expat)))) + +(define-public pgr-tk + (package + (name "pgr-tk") + (version "0.3.6") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Sema4-Research/pgr-tk") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0vm1k63v91zd0pfbg2zmwskajylz8xg83m63qxwaiwny5f4y6f1j")) + (snippet + #~(begin + (use-modules (guix build utils)) + (substitute* (find-files "." "Cargo.toml") + ;; Only use the major+minor version to decrease the number of + ;; special version crates. + (("(.*= \")([[:digit:]]+\\.[[:digit:]]+)\\.[[:digit:]]+(\".*)" + _ name version tail) + (string-append name version tail)) + ;; Then fix the version string for the actual package. + (("^version = \".*") + (string-append "version = \"" #$version "\"\n"))))))) + (build-system cargo-build-system) + (arguments + `(#:install-source? #f + #:cargo-test-flags + (list "--release" "--" + "--skip=get_aln_segements" + "--skip=get_shmmr_dots" + "--skip=AGCFile" + "--skip=SeqIndexDB") + #:cargo-inputs + (("rust-bindgen" ,rust-bindgen-0.58) + ("rust-bgzip" ,rust-bgzip-0.2) + ("rust-byteorder" ,rust-byteorder-1) + ("rust-clap" ,rust-clap-3) + ("rust-cuckoofilter" ,rust-cuckoofilter-0.5) + ("rust-flate2" ,rust-flate2-1) + ("rust-libc" ,rust-libc-0.2) + ("rust-log" ,rust-log-0.4) + ("rust-petgraph" ,rust-petgraph-0.6) + ("rust-pyo3" ,rust-pyo3-0.14) + ("rust-rayon" ,rust-rayon-1) + ("rust-regex" ,rust-regex-1) + ("rust-rustc-hash" ,rust-rustc-hash-1) + ("rust-serde" ,rust-serde-1) + ("rust-serde-json" ,rust-serde-json-1) + ("rust-simple-logger" ,rust-simple-logger-1)) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'insert-wfa-source + (lambda* (#:key inputs #:allow-other-keys) + (copy-recursively (assoc-ref inputs "wfa-src") + "rs-wfa/WFA"))) + (add-after 'unpack 'adjust-source + (lambda* (#:key inputs #:allow-other-keys) + (substitute* '("pgr-bin/build.rs" + "pgr-db/build.rs" + "pgr-tk/build.rs") + (("git") "ls") + (("bioconda") "Guix")) + ;; Build with zlib, not zlib-ng + (substitute* '("pgr-bin/Cargo.toml" + "pgr-db/Cargo.toml") + (("zlib-ng-compat") "zlib")) + ;; Don't look for agc to be bundled. + (substitute* "pgr-db/wrapper.h" + (("../agc/src/lib-cxx/agc-api.h") "lib-cxx/agc-api.h")) + (substitute* "pgr-db/build.rs" + ((".*panic!\\(\"Error.*") "")) + (mkdir-p "target/release") + (symlink (search-input-file inputs "/bin/agc") + "target/release/agc") + (symlink (search-input-file inputs "/lib/libagc.so") + "target/release/libagc"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (with-directory-excursion "target/release" + (install-file "libpgrtk.so" (string-append out "/lib")) + (for-each + (lambda (file) + (install-file file (string-append out "/bin"))) + (list "pgr-filter" + "pgr-mdb" + "pgr-multifilter" + "pgr-probe-match" + "pgr-shmmr-pair-count"))))))))) + (inputs + (list agc-for-pgr-tk + clang + python + zlib + (list zstd "lib"))) + (native-inputs + `(("pkg-config" ,pkg-config) + ("wfa-src" + ,(origin + (method git-fetch) + (uri (git-reference + ;; forPYO3 branch, 14-03-2021 + (url "https://github.com/cschin/WFA") + (commit "1f8c8d2905ed482cd2d306a1676d60c2a45cb098"))) + (file-name "wfa-for-pgr-tk") + (sha256 + (base32 "19h1cjp2bdlcfq5c6rsbk8bc0f8zn64b471dhj4xlfxd1prv2dpk")))))) + (home-page "https://github.com/Sema4-Research/pgr-tk") + (synopsis "Pangenome Research Tool Kit") + (description + "PGR-TK provides pangenome assembly management, query and +@acronym{Minimizer Anchored Pangenome, MAP} Graph Generation. It is a project +to provide Python and Rust libraries to facilitate pangenomics analysis. +Several algorithms and data structures used for the Peregrine Genome Assembler +are useful for Pangenomics analysis as well. This repo takes those algorithms +and data structure, combining other handy 3rd party tools to expose them as a +library in Python (with Rust code for those computing parts that need +performance.)") + (license (license:non-copyleft + "file:///LICENSE" + "CC-BY-NC-SA 4.0")))) + +(define-public graph-genotyper + (let ((commit "e7cc6b43a5b1f389d76bf9aac7f2ee02f92caeaf") ; October 17, 2022 + (revision "13")) + (package + (name "graph-genotyper") + (version (git-version "0.0.0" revision commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/davidebolo1993/graph_genotyper") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1l8yjpkqamiqr1q5i7vr5z04aba7skpbcwyc9dx5fiklvljjfhcx")))) + (build-system copy-build-system) + (arguments + `(#:install-plan + '(("genotype.py" "bin/") + ("genotype.sh" "bin/")) + #:phases + (modify-phases %standard-phases + (add-after 'install 'wrap-genotype + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((out (assoc-ref outputs "out"))) + (wrap-script (string-append out "/bin/genotype.sh") + `("GUIX_PYTHONPATH" ":" prefix (,(getenv "GUIX_PYTHONPATH"))) + `("PATH" ":" prefix + ,(map (lambda (file-name) + (string-append (assoc-ref inputs file-name) "/bin")) + (list "gafpack" + "odgi" + "python" + "samtools" + "vg")))))))))) + (inputs + (list gafpack + guile-3.0 + odgi + python + python-numpy + python-pandas + python-scipy + samtools + vg)) + (home-page "https://bitbucket.org/jana_ebler") + (synopsis "Genotyping based on k-mers and pangenome graphs") + (description + "This package provides a genotyper for various types of genetic variants +(such as SNPs, indels and structural variants). Genotypes are computed based on +read k-mer counts and a panel of known haplotypes. A description of the method +can be found @url{https://www.biorxiv.org/content/10.1101/2020.11.11.378133v1, +here}.") + (license (license:non-copyleft + "No license listed"))))) + (define-public pangenie (let ((commit "e779076827022d1416ab9fabf99a03d8f4725956") ; September 2, 2021 from phasing-tests branch (revision "2")) @@ -1490,20 +1790,9 @@ 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 python-pytest-runner-2 - (package - (inherit python-pytest-runner) - (version "2.12.2") - (source (origin - (method url-fetch) - (uri (pypi-uri "pytest-runner" version)) - (sha256 - (base32 - "11ivjj9hfphkv4yfb2g74av4yy86y8gcbf7gbif0p1hcdfnxg3w6")))))) - (define-public bh20-seq-resource - (let ((commit "ae4cb3c2cf7103bbc84f52618bb755d7ce25775b") - (revision "3")) + (let ((commit "2ae71911cd87ce4f2eabdff21e538267b3270d45") + (revision "4")) (package (name "bh20-seq-resource") (version (git-version "1.0" revision commit)) @@ -1514,36 +1803,45 @@ suitable for long reads, but works also well with short reads.") (commit commit))) (file-name (git-file-name name version)) (sha256 - (base32 "1k0gsz4yc8l5znanzd094g2jp40ksbpa9667zr31ayrjx6labz02")) + (base32 "1k6cc88hrcm77jwpdk2084q0zirv2vlbz3c07nmpbhk1lhqk5x0n")) (modules '((guix build utils))) (snippet '(begin - (substitute* "setup.py" - (("py-dateutil") "python-dateutil")) - #t)))) + (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 - `(("python-arvados-python-client" ,python-arvados-python-client) - ("python-dateutil" ,python-dateutil) - ("python-flask" ,python-flask) - ("python-magic" ,python-magic) - ("python-pyyaml" ,python-pyyaml) - ("python-pycurl" ,python-pycurl) - ("python-pyshex" ,python-pyshex) - ("python-redis" ,python-redis) - ("python-ruaml.yaml" ,python38-ruaml.yaml-0.15.76) - ("clustalw" ,clustalw) - ("python-schema-salad" ,python-schema-salad) - ("python-twint" ,python-twint) - ;; and for the service - ("python" ,python) - ("gunicorn" ,gunicorn))) + (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 - `(("git" ,(@ (gnu packages version-control) git)) - ("python-oauth2client" ,python-oauth2client) - ("python-pytest" ,python-pytest-4) - ("python-pytest-runner" ,python-pytest-runner-2) - ("python-uritemplate" ,python-uritemplate))) + (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") @@ -1553,6 +1851,18 @@ 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")) @@ -1593,6 +1903,56 @@ available to other researchers.") (delete-file "scanpy/tests/test_pca.py") #t))))))))) +;; TODO: Unbundle everything +(define-public odgi + (package + (name "odgi") + (version "0.8.1") + (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")) + (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"))))) + (build-system cmake-build-system) + (native-inputs + (list pkg-config)) + (inputs + (list jemalloc + libdivsufsort + pybind11 + python + sdsl-lite)) + (home-page "https://github.com/vgteam/odgi") + (synopsis "Optimized Dynamic Genome/Graph Implementation") + (description "@acronym{Optimized Dynamic Genome/Graph Implementation, odgi} +provides an efficient and succinct dynamic DNA sequence graph model, as well as +a host of algorithms that allow the use of such graphs in bioinformatic +analyses. + +Careful encoding of graph entities allows odgi to efficiently compute and +transform pangenomes with minimal overheads. @command{odgi} implements a +dynamic data structure that leveraged multi-core CPUs and can be updated on the +fly. + +The edges and path steps are recorded as deltas between the current node id and +the target node id, where the node id corresponds to the rank in the global +array of nodes. Graphs built from biological data sets tend to have local +partial order and, when sorted, the deltas be small. This allows them to be +compressed with a variable length integer representation, resulting in a small +in-memory footprint at the cost of packing and unpacking.") + (properties '((tunable? . #t))) + (license license:expat))) + (define-public vg (package (name "vg") @@ -1826,7 +2186,7 @@ available to other researchers.") (inputs `(("boost" ,boost) ("cairo" ,cairo) - ("curl" ,curl-minimal) + ("curl" ,curl) ("elfutils" ,elfutils) ("fastahack" ,fastahack) ("htslib" ,htslib) @@ -2055,7 +2415,7 @@ The Genome Browser itself does not draw conclusions; rather, it collates all relevant information in one location, leaving the exploration and interpretation to the user.") (license (list - license:bsd-0 ; kent/src/{utils,lib,inc,tabStorm,parasol,hg/ausoSql,hg/autoXml} + ;; license:bsd-0 ; kent/src/{utils,lib,inc,tabStorm,parasol,hg/ausoSql,hg/autoXml} license:bsd-3 ; these two for bundled htslib-1.3 license:expat (license:non-copyleft |