diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 684 |
1 files changed, 385 insertions, 299 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 86270ecc75..77af190659 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1,17 +1,17 @@ ;;; GNU Guix --- Functional package management for GNU -;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020 Ricardo Wurmus <rekado@elephly.net> +;;; Copyright © 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Ricardo Wurmus <rekado@elephly.net> ;;; Copyright © 2015, 2016, 2017, 2018 Ben Woodcroft <donttrustben@gmail.com> ;;; Copyright © 2015, 2016, 2018, 2019, 2020 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016, 2020 Roel Janssen <roel@gnu.org> -;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2016, 2017, 2018, 2019, 2020, 2021 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016, 2020 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2016, 2018 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> ;;; Copyright © 2018 Joshua Sierles, Nextjournal <joshua@nextjournal.com> ;;; Copyright © 2018 Gábor Boskovits <boskovits@gmail.com> -;;; Copyright © 2018, 2019, 2020 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> +;;; Copyright © 2018, 2019, 2020, 2021 Mădălin Ionel Patrașcu <madalinionel.patrascu@mdc-berlin.de> ;;; Copyright © 2019, 2020, 2021 Maxim Cournoyer <maxim.cournoyer@gmail.com> ;;; Copyright © 2019 Brian Leung <bkleung89@gmail.com> ;;; Copyright © 2019 Brett Gilio <brettg@gnu.org> @@ -57,6 +57,7 @@ #:use-module (guix build-system trivial) #:use-module (guix deprecation) #:use-module (gnu packages) + #:use-module (gnu packages assembly) #:use-module (gnu packages autotools) #:use-module (gnu packages algebra) #:use-module (gnu packages base) @@ -142,6 +143,7 @@ #:use-module (gnu packages xml) #:use-module (gnu packages xorg) #:use-module (srfi srfi-1) + #:use-module (srfi srfi-26) #:use-module (ice-9 match)) (define-public aragorn @@ -2770,6 +2772,86 @@ sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome.") (license license:gpl3+))) +(define-public trf + (package + (name "trf") + (version "4.09.1") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/Benson-Genomics-Lab/TRF") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0fhwr4s1mf8nw8fr5imwjvjr42b59p97zr961ifm8xl1bajz4wpg")))) + (build-system gnu-build-system) + (home-page "https://github.com/Benson-Genomics-Lab/TRF") + (synopsis "Tandem Repeats Finder: a program to analyze DNA sequences") + (description "A tandem repeat in DNA is two or more adjacent, approximate +copies of a pattern of nucleotides. Tandem Repeats Finder is a program to +locate and display tandem repeats in DNA sequences. In order to use the +program, the user submits a sequence in FASTA format. The output consists of +two files: a repeat table file and an alignment file. Submitted sequences may +be of arbitrary length. Repeats with pattern size in the range from 1 to 2000 +bases are detected.") + (license license:agpl3+))) + +(define-public repeat-masker + (package + (name "repeat-masker") + (version "4.1.1") + (source (origin + (method url-fetch) + (uri (string-append "http://www.repeatmasker.org/" + "RepeatMasker/RepeatMasker-" + version ".tar.gz")) + (sha256 + (base32 "03144sl9kh5ni2i33phi7x2pjndzbm5bjw3r4kqvmm6hxyb4k4x2")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #false ; there are none + #:phases + (modify-phases %standard-phases + (delete 'configure) + (replace 'build + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((share (string-append (assoc-ref outputs "out") + "/share/RepeatMasker"))) + (mkdir-p share) + (copy-recursively "." share) + (with-directory-excursion share + (invoke "perl" "configure" + "--trf_prgm" (which "trf") + "--hmmer_dir" + (string-append (assoc-ref inputs "hmmer") + "/bin")))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out")) + (share (string-append out "/share/RepeatMasker")) + (bin (string-append out "/bin")) + (path (getenv "PERL5LIB"))) + (install-file (string-append share "/RepeatMasker") bin) + (wrap-program (string-append bin "/RepeatMasker") + `("PERL5LIB" ":" prefix (,path ,share))))))))) + (inputs + `(("perl" ,perl) + ("perl-text-soundex" ,perl-text-soundex) + ("python" ,python) + ("python-h5py" ,python-h5py) + ("hmmer" ,hmmer) + ("trf" ,trf))) + (home-page "https://github.com/Benson-Genomics-Lab/TRF") + (synopsis "Tandem Repeats Finder: a program to analyze DNA sequences") + (description "A tandem repeat in DNA is two or more adjacent, approximate +copies of a pattern of nucleotides. Tandem Repeats Finder is a program to +locate and display tandem repeats in DNA sequences. In order to use the +program, the user submits a sequence in FASTA format. The output consists of +two files: a repeat table file and an alignment file. Submitted sequences may +be of arbitrary length. Repeats with pattern size in the range from 1 to 2000 +bases are detected.") + (license license:osl2.1))) + (define-public diamond (package (name "diamond") @@ -3508,61 +3590,60 @@ comment or quality sections.") (define-public gemma (package (name "gemma") - (version "0.98") + (version "0.98.3") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/xiangzhou/GEMMA") - (commit (string-append "v" version)))) + (url "https://github.com/genetics-statistics/GEMMA") + (commit version))) (file-name (git-file-name name version)) (sha256 (base32 - "1s3ncnbn45r2hh1cvrqky1kbqq6546biypr4f5mkw1kqlrgyh0yg")))) + "1p8a7kkfn1mmrg017aziy544aha8i9h6wd1x2dk3w2794wl33qb7")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "contrib") + #t)))) + (build-system gnu-build-system) (inputs - `(("eigen" ,eigen) - ("gfortran" ,gfortran "lib") - ("gsl" ,gsl) - ("lapack" ,lapack) + `(("gsl" ,gsl) ("openblas" ,openblas) ("zlib" ,zlib))) - (build-system gnu-build-system) + (native-inputs + `(("catch" ,catch-framework2-1) + ("perl" ,perl) + ("shunit2" ,shunit2) + ("which" ,which))) (arguments - `(#:make-flags - '(,@(match (%current-system) - ("x86_64-linux" - '("FORCE_DYNAMIC=1")) - ("i686-linux" - '("FORCE_DYNAMIC=1" "FORCE_32BIT=1")) - (_ - '("FORCE_DYNAMIC=1" "NO_INTEL_COMPAT=1")))) - #:phases + `(#:phases (modify-phases %standard-phases (delete 'configure) - (add-after 'unpack 'find-eigen + (add-after 'unpack 'prepare-build (lambda* (#:key inputs #:allow-other-keys) - ;; Ensure that Eigen headers can be found - (setenv "CPLUS_INCLUDE_PATH" - (string-append (assoc-ref inputs "eigen") - "/include/eigen3")) + (mkdir-p "bin") + (substitute* "Makefile" + (("/usr/local/opt/openblas") + (assoc-ref inputs "openblas"))) #t)) - (add-before 'build 'bin-mkdir - (lambda _ - (mkdir-p "bin") - #t)) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + ;; 'make slow-check' expects shunit2-2.0.3. + (with-directory-excursion "test" + (invoke "./test_suite.sh")) + #t))) (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((out (assoc-ref outputs "out"))) - (install-file "bin/gemma" - (string-append - out "/bin"))) - #t))) - #:tests? #f)) ; no tests included yet - (home-page "https://github.com/xiangzhou/GEMMA") + (install-file "bin/gemma" + (string-append (assoc-ref outputs "out") "/bin")) + #t))))) + (home-page "https://github.com/genetics-statistics/GEMMA") (synopsis "Tool for genome-wide efficient mixed model association") (description - "Genome-wide Efficient Mixed Model Association (GEMMA) provides a -standard linear mixed model resolver with application in genome-wide -association studies (GWAS).") + "@acronym{GEMMA, Genome-wide Efficient Mixed Model Association} provides a +standard linear mixed model resolver with application in @acronym{GWAS, +genome-wide association studies}.") (license license:gpl3))) (define-public grit @@ -4632,7 +4713,7 @@ sequencing tag position and orientation.") (define-public mafft (package (name "mafft") - (version "7.471") + (version "7.475") (source (origin (method url-fetch) (uri (string-append @@ -4641,7 +4722,7 @@ sequencing tag position and orientation.") (file-name (string-append name "-" version ".tgz")) (sha256 (base32 - "0r1973fx2scq4712zdqfy67wkzqj0c0bhrdy4jxhvq40mdxyry30")))) + "0i2i2m3blh2xkbkdk48hxfssks30ny0v381gdl7zwhcvp0axs26r")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; no automated tests, though there are tests in the read me @@ -6999,6 +7080,55 @@ sequence.") (supported-systems '("i686-linux" "x86_64-linux")) (license license:bsd-3))) +(define-public r-snapatac + (package + (name "r-snapatac") + (version "2.0") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/r3fang/SnapATAC") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "037jzlbl436fi7lkpq7d83i2vd1crnrik3vac2x6xj75dbikb2av")))) + (properties `((upstream-name . "SnapATAC"))) + (build-system r-build-system) + (propagated-inputs + `(("r-bigmemory" ,r-bigmemory) + ("r-doparallel" ,r-doparallel) + ("r-dosnow" ,r-dosnow) + ("r-edger" ,r-edger) + ("r-foreach" ,r-foreach) + ("r-genomicranges" ,r-genomicranges) + ("r-igraph" ,r-igraph) + ("r-iranges" ,r-iranges) + ("r-irlba" ,r-irlba) + ("r-matrix" ,r-matrix) + ("r-plyr" ,r-plyr) + ("r-plot3d" ,r-plot3d) + ("r-rann" ,r-rann) + ("r-raster" ,r-raster) + ("r-rcolorbrewer" ,r-rcolorbrewer) + ("r-rhdf5" ,r-rhdf5) + ("r-rtsne" ,r-rtsne) + ("r-scales" ,r-scales) + ("r-viridis" ,r-viridis))) + (home-page "https://github.com/r3fang/SnapATAC") + (synopsis "Single nucleus analysis package for ATAC-Seq") + (description + "This package provides a fast and accurate analysis toolkit for single +cell ATAC-seq (Assay for transposase-accessible chromatin using sequencing). +Single cell ATAC-seq can resolve the heterogeneity of a complex tissue and +reveal cell-type specific regulatory landscapes. However, the exceeding data +sparsity has posed unique challenges for the data analysis. This package +@code{r-snapatac} is an end-to-end bioinformatics pipeline for analyzing large- +scale single cell ATAC-seq data which includes quality control, normalization, +clustering analysis, differential analysis, motif inference and exploration of +single cell ATAC-seq sequencing data.") + (license license:gpl3))) + (define-public r-scde (package (name "r-scde") @@ -7065,6 +7195,45 @@ between two different types of motif instances using as much relevant information as possible.") (license (list license:gpl2+ license:gpl3+)))) +(define-public r-demultiplex + (let ((commit "6e2a1422c8e6f418cfb271997eebc91f9195f299") + (revision "1")) + (package + (name "r-demultiplex") + (version (git-version "1.0.2" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/chris-mcginnis-ucsf/MULTI-seq") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "01kv88wp8vdaq07sjk0d3d1cb553mq1xqg0war81pgmg63bgi38w")))) + (properties `((upstream-name . "deMULTIplex"))) + (build-system r-build-system) + (propagated-inputs + `(("r-kernsmooth" ,r-kernsmooth) + ("r-reshape2" ,r-reshape2) + ("r-rtsne" ,r-rtsne) + ("r-shortread" ,r-shortread) + ("r-stringdist" ,r-stringdist))) + (home-page "https://github.com/chris-mcginnis-ucsf/MULTI-seq") + (synopsis "MULTI-seq pre-processing and classification tools") + (description + "deMULTIplex is an R package for analyzing single-cell RNA sequencing +data generated with the MULTI-seq sample multiplexing method. The package +includes software to + +@enumerate +@item Convert raw MULTI-seq sample barcode library FASTQs into a sample + barcode UMI count matrix, and +@item Classify cell barcodes into sample barcode groups. +@end enumerate +") + (license license:cc0)))) + (define-public r-genefilter (package (name "r-genefilter") @@ -7652,6 +7821,31 @@ BLAST, KEGG, GenBank, MEDLINE and GO.") ;; (LGPLv2.1+) and scripts in samples (which have GPL2 and GPL2+) (license (list license:ruby license:lgpl2.1+ license:gpl2+ )))) +(define-public bio-vcf + (package + (name "bio-vcf") + (version "0.9.5") + (source + (origin + (method url-fetch) + (uri (rubygems-uri "bio-vcf" version)) + (sha256 + (base32 + "1glw5pn9s8z13spxk6yyfqaz80n9lga67f33w35nkpq9dwi2vg6g")))) + (build-system ruby-build-system) + (native-inputs + `(("ruby-cucumber" ,ruby-cucumber))) + (synopsis "Smart VCF parser DSL") + (description + "Bio-vcf provides a @acronym{DSL, domain specific language} for processing +the VCF format. Record named fields can be queried with regular expressions. +Bio-vcf is a new generation VCF parser, filter and converter. Bio-vcf is not +only very fast for genome-wide (WGS) data, it also comes with a filtering, +evaluation and rewrite language and can output any type of textual data, +including VCF header and contents in RDF and JSON.") + (home-page "https://github.com/vcflib/bio-vcf") + (license license:expat))) + (define-public r-biocviews (package (name "r-biocviews") @@ -9312,8 +9506,9 @@ group or two ChIP groups run under different conditions.") (delete 'configure) ; There is no configure phase. (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (install-file "filevercmp" bin) + (let ((out (assoc-ref outputs "out"))) + (install-file "filevercmp" (string-append out "/bin")) + (install-file "filevercmp.h" (string-append out "/include")) #t)))))) (home-page "https://github.com/ekg/filevercmp") (synopsis "This program compares version strings") @@ -10440,41 +10635,20 @@ explore and perform basic analysis of single cell sequencing data coming from droplet sequencing. It has been particularly tailored for Drop-seq.") (license license:gpl3)))) -(define htslib-for-sambamba - (let ((commit "2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5")) - (package - (inherit htslib) - (name "htslib-for-sambamba") - (version (string-append "1.3.1-1." (string-take commit 9))) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/lomereiter/htslib") - (commit commit))) - (file-name (string-append "htslib-" version "-checkout")) - (sha256 - (base32 - "0g38g8s3npr0gjm9fahlbhiskyfws9l5i0x1ml3rakzj7az5l9c9")))) - (native-inputs - `(("autoconf" ,autoconf) - ("automake" ,automake) - ,@(package-native-inputs htslib)))))) - (define-public sambamba (package (name "sambamba") - (version "0.7.1") + (version "0.8.0") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/lomereiter/sambamba") + (url "https://github.com/biod/sambamba") (commit (string-append "v" version)))) - (file-name (string-append name "-" version "-checkout")) + (file-name (git-file-name name version)) (sha256 (base32 - "111h05b60pj8dxbidiamy4imc92x2962b3lmb7wgysl6lx064qis")))) + "07dznzl6m8k7sw84jxw2kx6i3ymrapbmcmyh0fxz8wrybhw8fmwc")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there is no test target @@ -10484,52 +10658,30 @@ droplet sequencing. It has been particularly tailored for Drop-seq.") (delete 'configure) (add-after 'unpack 'fix-ldc-version (lambda _ - (substitute* "gen_ldc_version_info.py" - (("/usr/bin/env.*") (which "python3"))) (substitute* "Makefile" ;; We use ldc2 instead of ldmd2 to compile sambamba. (("\\$\\(shell which ldmd2\\)") (which "ldc2"))) #t)) - (add-after 'unpack 'place-biod-and-undead - (lambda* (#:key inputs #:allow-other-keys) - (copy-recursively (assoc-ref inputs "biod") "BioD") - #t)) (add-after 'unpack 'unbundle-prerequisites (lambda _ (substitute* "Makefile" - (("htslib/libhts.a lz4/lib/liblz4.a") - "-L-lhts -L-llz4") - ((" lz4-static htslib-static") "")) + (("= lz4/lib/liblz4.a") "= -L-llz4") + (("ldc_version_info lz4-static") "ldc_version_info")) #t)) (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin"))) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) (mkdir-p bin) (copy-file (string-append "bin/sambamba-" ,version) (string-append bin "/sambamba")) #t)))))) (native-inputs - `(("ldc" ,ldc) - ("rdmd" ,rdmd) - ("python" ,python) - ("biod" - ,(let ((commit "7969eb0a847b05874e83ffddead26e193ece8101")) - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/biod/BioD") - (commit commit))) - (file-name (string-append "biod-" - (string-take commit 9) - "-checkout")) - (sha256 - (base32 - "0mjxsmbmv0jxl3pq21p8j5r829d648if8q58ka50b2956lc6qkpm"))))))) + `(("python" ,python))) (inputs - `(("lz4" ,lz4) - ("htslib" ,htslib-for-sambamba))) - (home-page "https://lomereiter.github.io/sambamba/") + `(("ldc" ,ldc) + ("lz4" ,lz4) + ("zlib" ,zlib))) + (home-page "https://github.com/biod/sambamba") (synopsis "Tools for working with SAM/BAM data") (description "Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for @@ -14773,10 +14925,14 @@ some of the details of opening and jumping in tabix-indexed files.") (delete 'configure) ; There is no configure phase. (replace 'install (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (let* ((out (assoc-ref outputs "out")) + (bin (string-append out "/bin")) + (include (string-append out "/include"))) ;; TODO: There are Python modules for these programs too. (install-file "multichoose" bin) - (install-file "multipermute" bin)) + (install-file "multipermute" bin) + (install-file "multichoose.h" include) + (install-file "multipermute.h" include)) #t))))) (home-page "https://github.com/ekg/multichoose") (synopsis "Efficient loopless multiset combination generation algorithm") @@ -14885,32 +15041,44 @@ library automatically handles index file generation and use.") (define-public vcflib (package (name "vcflib") - (version "1.0.1") + (version "1.0.2") (source (origin - (method url-fetch) - (uri (string-append "https://github.com/vcflib/vcflib/releases/" - "download/v" version - "/vcflib-" version "-src.tar.gz")) + (method git-fetch) + (uri (git-reference + (url "https://github.com/vcflib/vcflib") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) (sha256 - (base32 "14zzrg8hg8cq9cvq2wdvp21j7nmxxkjrbagw2apd2yqv2kyx42lm")) - (patches (search-patches "vcflib-use-shared-libraries.patch")) + (base32 "1k1z3876kbzifj1sqfzsf3lgb4rw779hvkg6ryxbyq5bc2paj9kh")) (modules '((guix build utils))) (snippet - `(begin + '(begin + (substitute* "CMakeLists.txt" + ((".*fastahack.*") "") + ((".*smithwaterman.*") "") + (("(pkg_check_modules\\(TABIXPP)" text) + (string-append + "pkg_check_modules(FASTAHACK REQUIRED fastahack)\n" + "pkg_check_modules(SMITHWATERMAN REQUIRED smithwaterman)\n" + text)) + (("\\$\\{TABIXPP_LIBRARIES\\}" text) + (string-append "${FASTAHACK_LIBRARIES} " + "${SMITHWATERMAN_LIBRARIES} " + text))) (substitute* (find-files "." "\\.(h|c)(pp)?$") (("\"SmithWatermanGotoh.h\"") "<smithwaterman/SmithWatermanGotoh.h>") (("\"convert.h\"") "<smithwaterman/convert.h>") (("\"disorder.h\"") "<smithwaterman/disorder.h>") - (("\"tabix.hpp\"") "<tabix.hpp>") - (("\"Fasta.h\"") "<fastahack/Fasta.h>")) + (("Fasta.h") "fastahack/Fasta.h")) (for-each delete-file-recursively '("fastahack" "filevercmp" "fsom" "googletest" "intervaltree" - "libVCFH" "multichoose" "smithwaterman" "tabixpp")) + "libVCFH" "multichoose" "smithwaterman")) #t)))) - (build-system gnu-build-system) + (build-system cmake-build-system) (inputs - `(("htslib" ,htslib) + `(("bzip2" ,bzip2) + ("htslib" ,htslib) ("fastahack" ,fastahack) ("perl" ,perl) ("python" ,python) @@ -14923,22 +15091,20 @@ library automatically handles index file generation and use.") ;; Submodules. ;; This package builds against the .o files so we need to extract the source. ("filevercmp-src" ,(package-source filevercmp)) + ("fsom-src" ,(package-source fsom)) ("intervaltree-src" ,(package-source intervaltree)) ("multichoose-src" ,(package-source multichoose)))) (arguments `(#:tests? #f ; no tests #:phases (modify-phases %standard-phases - (add-after 'unpack 'set-flags - (lambda* (#:key outputs #:allow-other-keys) - (substitute* "Makefile" - (("LDFLAGS =") - (string-append "LDFLAGS = -Wl,-rpath=" - (assoc-ref outputs "out") "/lib "))) - (substitute* "filevercmp/Makefile" - (("-c") "-c -fPIC")) + (add-after 'unpack 'build-shared-library + (lambda _ + (substitute* "CMakeLists.txt" + (("vcflib STATIC") "vcflib SHARED")) + (substitute* "test/Makefile" + (("libvcflib.a") "libvcflib.so")) #t)) - (delete 'configure) (add-after 'unpack 'unpack-submodule-sources (lambda* (#:key inputs #:allow-other-keys) (let ((unpack (lambda (source target) @@ -14951,39 +15117,31 @@ library automatically handles index file generation and use.") "--strip-components=1")))))) (and (unpack "filevercmp-src" "filevercmp") + (unpack "fsom-src" "fsom") (unpack "intervaltree-src" "intervaltree") - (unpack "multichoose-src" "multichoose"))))) - (replace 'install + (unpack "multichoose-src" "multichoose")) + #t))) + ;; This pkg-config file is provided by other distributions. + (add-after 'install 'install-pkg-config-file (lambda* (#:key outputs #:allow-other-keys) (let* ((out (assoc-ref outputs "out")) - (bin (string-append out "/bin")) - (lib (string-append out "/lib"))) - (for-each (lambda (file) - (install-file file bin)) - (find-files "bin" ".*")) - (install-file "libvcflib.so" lib) - (install-file "libvcflib.a" lib) - (for-each - (lambda (file) - (install-file file (string-append out "/include"))) - (find-files "include" "\\.h(pp)?$")) - (mkdir-p (string-append lib "/pkgconfig")) - (with-output-to-file (string-append lib "/pkgconfig/vcflib.pc") + (pkgconfig (string-append out "/lib/pkgconfig"))) + (mkdir-p pkgconfig) + (with-output-to-file (string-append pkgconfig "/vcflib.pc") (lambda _ (format #t "prefix=~a~@ exec_prefix=${prefix}~@ libdir=${exec_prefix}/lib~@ includedir=${prefix}/include~@ ~@ - ~@ - Name: libvcflib~@ + Name: vcflib~@ Version: ~a~@ - Requires: smithwaterman, fastahack~@ + Requires: smithwaterman, fastahack, tabixpp~@ Description: C++ library for parsing and manipulating VCF files~@ Libs: -L${libdir} -lvcflib~@ Cflags: -I${includedir}~%" - out ,version)))) - #t))))) + out ,version))) + #t)))))) (home-page "https://github.com/vcflib/vcflib/") (synopsis "Library for parsing and manipulating VCF files") (description "Vcflib provides methods to manipulate and interpret @@ -14994,125 +15152,94 @@ manipulations on VCF files.") (license license:expat))) (define-public freebayes - (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb") - (revision "1") - (version "1.0.2")) - (package - (name "freebayes") - (version (git-version version revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/freebayes") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2")))) - (build-system gnu-build-system) - (inputs - `(("bamtools" ,bamtools) - ("htslib" ,htslib) - ("zlib" ,zlib))) - (native-inputs - `(("bc" ,bc) ; Needed for running tests. - ("samtools" ,samtools) ; Needed for running tests. - ("parallel" ,parallel) ; Needed for running tests. - ("perl" ,perl) ; Needed for running tests. - ("procps" ,procps) ; Needed for running tests. - ("python" ,python-2) ; Needed for running tests. - ("vcflib-src" ,(package-source vcflib)) - ;; These are submodules for the vcflib version used in freebayes. - ;; This package builds against the .o files so we need to extract the source. - ("tabixpp-src" ,(package-source tabixpp)) - ("smithwaterman-src" ,(package-source smithwaterman)) - ("multichoose-src" ,(package-source multichoose)) - ("fsom-src" ,(package-source fsom)) - ("filevercmp-src" ,(package-source filevercmp)) - ("fastahack-src" ,(package-source fastahack)) - ("intervaltree-src" ,(package-source intervaltree)) - ;; These submodules are needed to run the tests. - ("bash-tap-src" ,(package-source bash-tap)) - ("test-simple-bash-src" - ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ingydotnet/test-simple-bash/") - (commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc"))) - (file-name "test-simple-bash-src-checkout") - (sha256 - (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga")))))) - (arguments - `(#:make-flags - (list "CC=gcc" - (string-append "BAMTOOLS_ROOT=" - (assoc-ref %build-inputs "bamtools"))) - #:test-target "test" - #:phases - (modify-phases %standard-phases - (delete 'configure) - (add-after 'unpack 'fix-tests - (lambda _ - (substitute* "test/t/01_call_variants.t" - (("grep -P \"\\(\\\\t500\\$\\|\\\\t11000\\$\\|\\\\t1000\\$\\)\"") - "grep -E ' (500|11000|1000)$'")) - #t)) - (add-after 'unpack 'unpack-submodule-sources - (lambda* (#:key inputs #:allow-other-keys) - (let ((unpack (lambda (source target) - (with-directory-excursion target - (if (file-is-directory? (assoc-ref inputs source)) - (copy-recursively (assoc-ref inputs source) ".") - (invoke "tar" "xvf" - (assoc-ref inputs source) - "--strip-components=1")))))) - (and - (unpack "vcflib-src" "vcflib") - (unpack "fastahack-src" "vcflib/fastahack") - (unpack "filevercmp-src" "vcflib/filevercmp") - (unpack "fsom-src" "vcflib/fsom") - (unpack "intervaltree-src" "vcflib/intervaltree") - (unpack "multichoose-src" "vcflib/multichoose") - (unpack "smithwaterman-src" "vcflib/smithwaterman") - (unpack "tabixpp-src" "vcflib/tabixpp") - (unpack "test-simple-bash-src" "test/test-simple-bash") - (unpack "bash-tap-src" "test/bash-tap"))))) - (add-after 'unpack-submodule-sources 'fix-makefiles - (lambda _ - ;; We don't have the .git folder to get the version tag from. - (substitute* "vcflib/Makefile" - (("^GIT_VERSION.*") - (string-append "GIT_VERSION = v" ,version))) - (substitute* "src/Makefile" - (("-I\\$\\(BAMTOOLS_ROOT\\)/src") - "-I$(BAMTOOLS_ROOT)/include/bamtools")) - #t)) - (add-before 'build 'build-tabixpp-and-vcflib - (lambda* (#:key inputs make-flags #:allow-other-keys) - (with-directory-excursion "vcflib" - (with-directory-excursion "tabixpp" - (apply invoke "make" - (string-append "HTS_LIB=" - (assoc-ref inputs "htslib") - "/lib/libhts.a") - make-flags)) - (apply invoke "make" - (string-append "CFLAGS=-Itabixpp") - "all" - make-flags)))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) - (install-file "bin/freebayes" bin) - (install-file "bin/bamleftalign" bin)) - #t))))) - (home-page "https://github.com/ekg/freebayes") - (synopsis "Haplotype-based variant detector") - (description "FreeBayes is a Bayesian genetic variant detector designed to + (package + (name "freebayes") + (version "1.3.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/freebayes/freebayes") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0myz3giad7jqp6ricdfnig9ymlcps2h67mlivadvx97ngagm85z8")) + (patches (search-patches "freebayes-devendor-deps.patch")) + (modules '((guix build utils))) + (snippet + '(begin + (delete-file-recursively "contrib/htslib") + #t)))) + (build-system meson-build-system) + (inputs + `(("fastahack" ,fastahack) + ("htslib" ,htslib) + ("smithwaterman" ,smithwaterman) + ("tabixpp" ,tabixpp) + ("vcflib" ,vcflib) + ("zlib" ,zlib))) + (native-inputs + `(("bash-tap" ,bash-tap) + ("bc" ,bc) + ("grep" ,grep) ; Built with perl support. + ("parallel" ,parallel) + ("perl" ,perl) + ("pkg-config" ,pkg-config) + ("samtools" ,samtools) + ("simde" ,simde) + ;; This submodule is needed to run the tests. + ("test-simple-bash-src" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ingydotnet/test-simple-bash/") + (commit "124673ff204b01c8e96b7fc9f9b32ee35d898acc"))) + (file-name "test-simple-bash-src-checkout") + (sha256 + (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga")))))) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'unpack 'patch-source + (lambda* (#:key inputs #:allow-other-keys) + (let ((bash-tap (assoc-ref inputs "bash-tap"))) + (substitute* (find-files "test/t") + (("BASH_TAP_ROOT=bash-tap") + (string-append "BASH_TAP_ROOT=" bash-tap "/bin")) + (("bash-tap/bash-tap-bootstrap") + (string-append bash-tap "/bin/bash-tap-bootstrap")) + (("source.*bash-tap-bootstrap") + (string-append "source " bash-tap "/bin/bash-tap-bootstrap"))) + (substitute* "meson.build" + ;; Some inputs aren't actually needed. + ((".*bamtools/src.*") "") + ((".*multichoose.*") "")) + (substitute* '("src/BedReader.cpp" + "src/BedReader.h") + (("../intervaltree/IntervalTree.h") "IntervalTree.h")) + #t))) + (add-after 'unpack 'unpack-submodule-sources + (lambda* (#:key inputs #:allow-other-keys) + (mkdir-p "test/test-simple-bash") + (copy-recursively (assoc-ref inputs "test-simple-bash-src") + "test/test-simple-bash") + #t)) + ;; The slow tests take longer than the specified timeout. + ,@(if (any (cute string=? <> (%current-system)) + '("armhf-linux" "aarch64-linux")) + '((replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "meson" "test" "--timeout-multiplier" "5")) + #t))) + '())))) + (home-page "https://github.com/freebayes/freebayes") + (synopsis "Haplotype-based variant detector") + (description "FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.") - (license license:expat)))) + (license license:expat))) (define-public samblaster (package @@ -15398,44 +15525,3 @@ biological processes. SBML is useful for models of metabolism, cell signaling, and more. It continues to be evolved and expanded by an international community.") (license license:lgpl2.1+))) - -(define-public grocsvs - ;; The last release is out of date and new features have been added. - (let ((commit "ecd956a65093a0b2c41849050e4512d46fecea5d") - (revision "1")) - (package - (name "grocsvs") - (version (git-version "0.2.6.1" revision commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/grocsvs/grocsvs") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "14505725gr7qxc17cxxf0k6lzcwmgi64pija4mwf29aw70qn35cc")) - (patches (search-patches "grocsvs-dont-use-admiral.patch")))) - (build-system python-build-system) - (arguments - `(#:tests? #f ; No test suite. - #:python ,python-2)) ; Only python-2 supported. - (inputs - `(("python2-h5py" ,python2-h5py) - ("python2-ipython-cluster-helper" ,python2-ipython-cluster-helper) - ("python2-networkx" ,python2-networkx) - ("python2-psutil" ,python2-psutil) - ("python2-pandas" ,python2-pandas) - ("python2-pybedtools" ,python2-pybedtools) - ("python2-pyfaidx" ,python2-pyfaidx) - ("python2-pygraphviz" ,python2-pygraphviz) - ("python2-pysam" ,python2-pysam) - ("python2-scipy" ,python2-scipy))) - (home-page "https://github.com/grocsvs/grocsvs") - (synopsis "Genome-wide reconstruction of complex structural variants") - (description - "@dfn{Genome-wide Reconstruction of Complex Structural Variants} -(GROC-SVs) is a software pipeline for identifying large-scale structural -variants, performing sequence assembly at the breakpoints, and reconstructing -the complex structural variants using the long-fragment information from the -10x Genomics platform.") - (license license:expat)))) |