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-rw-r--r--gn/packages/bioinformatics.scm444
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