From d9340de9031211c220b5b710e64af29e066f26f2 Mon Sep 17 00:00:00 2001 From: Brian Leung Date: Tue, 25 Jun 2019 20:48:54 +0200 Subject: gnu: khmer: Make gzip timestamps writable. * gnu/packages/bioinformatics.scm (khmer)[arguments]: Add custom phase to make gzip timestamps writable. Signed-off-by: Efraim Flashner --- gnu/packages/bioinformatics.scm | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 89f1ac36ea..bcec9cd279 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13,6 +13,7 @@ ;;; Copyright © 2018 Gábor Boskovits ;;; Copyright © 2018 Mădălin Ionel Patrașcu ;;; Copyright © 2019 Maxim Cournoyer +;;; Copyright © 2019 Brian Leung ;;; ;;; This file is part of GNU Guix. ;;; @@ -4206,8 +4207,15 @@ command, or queried for specific k-mers with @code{jellyfish query}.") (modify-phases %standard-phases (add-after 'unpack 'set-cc (lambda _ (setenv "CC" "gcc") #t)) - ;; FIXME: This fails with "permission denied". - (delete 'reset-gzip-timestamps)))) + + (add-before 'reset-gzip-timestamps 'make-files-writable + (lambda* (#:key outputs #:allow-other-keys) + ;; Make sure .gz files are writable so that the + ;; 'reset-gzip-timestamps' phase can do its work. + (let ((out (assoc-ref outputs "out"))) + (for-each make-file-writable + (find-files out "\\.gz$")) + #t)))))) (native-inputs `(("python-cython" ,python-cython) ("python-pytest" ,python-pytest) -- cgit v1.2.3 From 8a5f9d3d56b76ef8800ac8b67a5bdcbc4763fb92 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Aug 2019 15:39:36 +0200 Subject: gnu: r-edger: Update to 3.26.6. * gnu/packages/bioinformatics.scm (r-edger): Update to 3.26.6. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bcec9cd279..bb08ff89ff 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7458,13 +7458,13 @@ names in their natural, rather than lexicographic, order.") (define-public r-edger (package (name "r-edger") - (version "3.26.5") + (version "3.26.6") (source (origin (method url-fetch) (uri (bioconductor-uri "edgeR" version)) (sha256 (base32 - "0iba4krz30dx5b0s89n5cfkwn64867s7vmvvfqms9lbcr4kj439m")))) + "17vadhamjv4x0l4qqq2p2fi6j2bkllz5zd8dq761vgd5ic23zizm")))) (properties `((upstream-name . "edgeR"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From fbd761fe9bb4182a41e02d377723b21afc1abacd Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Aug 2019 15:39:48 +0200 Subject: gnu: r-limma: Update to 3.40.6. * gnu/packages/bioinformatics.scm (r-limma): Update to 3.40.6. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index bb08ff89ff..604c245375 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7525,13 +7525,13 @@ coding changes and predict coding outcomes.") (define-public r-limma (package (name "r-limma") - (version "3.40.2") + (version "3.40.6") (source (origin (method url-fetch) (uri (bioconductor-uri "limma" version)) (sha256 (base32 - "1d4ig2b7fa9mwja52isxrwmprfdjdk1mlcf2skhdp51l24z6wbk7")))) + "166z8cdh6w90rldqqaar7hyaskwiy4smawjfbn4sn58clv6q3mp8")))) (build-system r-build-system) (home-page "http://bioinf.wehi.edu.au/limma") (synopsis "Package for linear models for microarray and RNA-seq data") -- cgit v1.2.3 From 2ebd2b440daeb356f7088fe67ee2ee271971ee75 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Aug 2019 15:39:54 +0200 Subject: gnu: r-biomart: Update to 2.40.3. * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.40.3. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 604c245375..580bffe784 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7658,13 +7658,13 @@ annotation data packages using SQLite data storage.") (define-public r-biomart (package (name "r-biomart") - (version "2.40.1") + (version "2.40.3") (source (origin (method url-fetch) (uri (bioconductor-uri "biomaRt" version)) (sha256 (base32 - "1abl0c4qbhfqf9ixdp74183phm7s8rszrr5ldczm59b8vyng8rhx")))) + "022m1r44s00c5k9bmv0lr22lcn662nhc91aazvv0yyysxjamyf60")))) (properties `((upstream-name . "biomaRt"))) (build-system r-build-system) -- cgit v1.2.3 From 6f8760d9f8a982282bf0eecedad4e5cf5ae6ca3b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Aug 2019 15:40:00 +0200 Subject: gnu: r-summarizedexperiment: Update to 1.14.1. * gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.14.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 580bffe784..a91dd12993 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7819,13 +7819,13 @@ array-like objects like @code{DataFrame} objects (typically with Rle columns), (define-public r-summarizedexperiment (package (name "r-summarizedexperiment") - (version "1.14.0") + (version "1.14.1") (source (origin (method url-fetch) (uri (bioconductor-uri "SummarizedExperiment" version)) (sha256 (base32 - "1ypk63pdml89y81pr41i2zq0fimsaxsa5lgpg6xs5cwikyaq0pci")))) + "0bhwgzrdipr0qjzc4j0qspqprx3v1rvshmx4j6506dv43pqlgp3f")))) (properties `((upstream-name . "SummarizedExperiment"))) (build-system r-build-system) -- cgit v1.2.3 From e16fe0b50af2df01cafd6a0f6413597e483ae2db Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Aug 2019 15:40:13 +0200 Subject: gnu: r-rtracklayer: Update to 1.44.2. * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.44.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a91dd12993..afe72631be 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7883,13 +7883,13 @@ alignments.") (define-public r-rtracklayer (package (name "r-rtracklayer") - (version "1.44.0") + (version "1.44.2") (source (origin (method url-fetch) (uri (bioconductor-uri "rtracklayer" version)) (sha256 (base32 - "161gcks9b12993g9k27gf7wfh8lgd8m8rr7x2slgfqqssk0yrmpd")))) + "03b4rfsbzjjf5kxcsjv7kq8hrsgcvz9rfzcn2v7fx3nr818pbb8s")))) (build-system r-build-system) (arguments `(#:phases -- cgit v1.2.3 From 76d9b08e1b4677dbcb8fbbb8e607ceb35fe81d80 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Aug 2019 15:40:31 +0200 Subject: gnu: r-genomicfeatures: Update to 1.36.4. * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.36.4. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index afe72631be..4ebd891ad9 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7930,13 +7930,13 @@ as well as query and modify the browser state, such as the current viewport.") (define-public r-genomicfeatures (package (name "r-genomicfeatures") - (version "1.36.3") + (version "1.36.4") (source (origin (method url-fetch) (uri (bioconductor-uri "GenomicFeatures" version)) (sha256 (base32 - "0zkd57i5qjxsravv0gbyckc0wrnqzgxd61ibh3jmhmrccrr9ihn3")))) + "0mzqv8pyxx5nwchyx3radym9ws2f9hb50xc9abjsjs4w4pv91j3k")))) (properties `((upstream-name . "GenomicFeatures"))) (build-system r-build-system) -- cgit v1.2.3 From afe4be49f1346f11a3ac85884afef4434dafa7e4 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Aug 2019 15:40:38 +0200 Subject: gnu: r-rcas: Update to 1.10.1. * gnu/packages/bioinformatics.scm (r-rcas): Update to 1.10.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4ebd891ad9..3661f9f5c1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -8354,13 +8354,13 @@ paired-end data.") (define-public r-rcas (package (name "r-rcas") - (version "1.10.0") + (version "1.10.1") (source (origin (method url-fetch) (uri (bioconductor-uri "RCAS" version)) (sha256 (base32 - "1h4vf5gzilqbdrd8m9l3zc2m4sca8cir8366a7njgd558k7ld5kl")))) + "06z5zmdi34jblw37z6ff8hb6lvvi0chwr37acwqfn8d27ax9lakz")))) (properties `((upstream-name . "RCAS"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From c8e141ab02c0f5d4027b8b4d0eb141796d4f0ffc Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Tue, 6 Aug 2019 15:40:46 +0200 Subject: gnu: r-msnid: Update to 1.18.1. * gnu/packages/bioinformatics.scm (r-msnid): Update to 1.18.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3661f9f5c1..956257d7bb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -9418,14 +9418,14 @@ of mass spectrometry based proteomics data.") (define-public r-msnid (package (name "r-msnid") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "MSnID" version)) (sha256 (base32 - "18mp8zacawhfapfwpq8czbswxix2ykvqhwjga54v0a99zg3k87h3")))) + "1n49l5mjdz7p4g2nwsbhm1jcj42sv6lsriq77n2imvacsvk0qfmb")))) (properties `((upstream-name . "MSnID"))) (build-system r-build-system) (propagated-inputs -- cgit v1.2.3 From a1eb8be8ca1a0a4c952f264f8846b67a32db0ec8 Mon Sep 17 00:00:00 2001 From: Robert Vollmert Date: Thu, 4 Jul 2019 09:57:31 +0200 Subject: gnu: Remove ghc-parsec, ghc-stm, ghc-text, ghc-xhtml. These are ghc-8.4-bundled packages, removing to avoid build conflicts. * gnu/packages/haskell.scm (ghc-parsec, ghc-stm, ghc-text): Remove. * gnu/packages/haskell-web.scm (ghc-xhtml): Remove. * gnu/packages/agda.scm (agda)[inputs]: Remove ghc-stm and ghc-text. * gnu/packages/bioinformatics.scm (ngless)[inputs]: Remove ghc-parsec and ghc-text. * gnu/packages/haskell-apps.scm (darcs)[inputs]: Remove ghc-parsec. (git-annex)[inputs]: Remove ghc-stm and ghc-text. (ghc-sdl2)[inputs]: Remove ghc-text. (ghc-sdl2-image)[inputs]: Remove ghc-text. * gnu/packages/haskell-check.scm (ghc-tasty-ant-xml)[inputs]: Remove ghc-stm. (ghc-tasty)[inputs]: Remove ghc-stm. (ghc-tasty-rerun)[inputs]: Same. (ghc-quickcheck-instances)[inputs]: Remove ghc-text. (ghc-hedgehog)[inputs]: Remove ghc-stm. * gnu/packages/haskell-crypto.scm (ghc-asn1-encoding)[inputs]: Remove ghc-text. * gnu/packages/haskell-web.scm (ghc-tagsoup)[inputs]: Remove ghc-text. (ghc-cookie)[inputs]: Same. (ghc-http-types)[inputs]: Same. (ghc-http)[inputs]: Remove ghc-parsec. (ghc-http-client)[inputs]: Remove ghc-text. (ghc-http2)[inputs]: Remove ghc-stm. (ghc-http-conduit)[native-inputs]: Remove ghc-text. (ghc-wai)[inputs]: Same. (ghc-wai-extra)[inputs]: Same. (ghc-warp)[inputs]: Remove ghc-stm and ghc-text. (ghc-xss-sanitize)[native-inputs]: Remove ghc-text. (ghc-css-text)[inputs]: Same. (ghc-mime-types)[inputs]: Same. (ghc-blaze-html)[inputs]: Same. (ghc-aeson)[inputs]: Same. (ghc-aeson-pretty)[inputs]: Same. (ghc-aeson-qq)[inputs]: Remove ghc-text and ghc-parsec. (ghc-multipart)[inputs]: Remove ghc-parsec. (ghc-uri-encode)[inputs]: Remove ghc-text. (ghc-path-pieces)[inputs]: Same. (ghc-yesod-core)[inputs]: Remove ghc-text and ghc-parsec. (ghc-yesod-persistent)[inputs]: Remove ghc-text. (ghc-yesod-form)[inputs]: Same. (ghc-yesod)[inputs]: Same. (ghc-hxt-regex-xmlschema)[inputs]: Remove ghc-parsec and ghc-text. (ghc-hxt)[inputs]: Remove ghc-parsec. * gnu/packages/haskell.scm (ghc-convertible)[inputs]: Remove ghc-text. (ghc-double-conversion)[inputs]: Same. (ghc-tree-diff)[inputs]: Remove ghc-parsec and ghc-text. [native-inputs]: Remove ghc-parsec. (ghc-cgi)[inputs]: Remove ghc-parsec. (hlint)[inputs]: Remove ghc-text. (ghc-openglraw)[inputs]: Remove ghc-text. (ghc-opengl)[inputs]: Same. (ghc-streaming-commons)[inputs]: Remove ghc-stm and ghc-text. (ghc-hackage-security)[inputs]: Remove ghc-parsec. (cabal-install)[inputs]: Remove ghc-stm. (ghc-parsec-numbers)[inputs]: Remove ghc-parsec. (ghc-safesemaphore)[inputs]: Remove ghc-stm. (ghc-text-binary)[inputs]: Remove ghc-text. (ghc-hashable)[inputs]: Remove ghc-text. (ghc-transformers-base)[inputs]: Remove ghc-stm. (ghc-indents)[inputs]: Remove ghc-parsec. (ghc-regex-tdfa-rc)[inputs]: Same. (ghc-regex-tdfa-text)[inputs]: Same. (ghc-regex)[inputs]: Remove ghc-text. (ghc-parsers)[inputs]: Remove ghc-parsec and ghc-text. (ghc-attoparsec)[inputs]: Remove ghc-text. (ghc-attoparsec-bootstrap)[inputs]: Same. (ghc-zip-archive)[inputs]: Same. (ghc-polyparse)[inputs]: Same. (ghc-reducers)[inputs]: Same. (ghc-xml)[inputs]: Same. (ghc-feed)[inputs]: Same. (ghc-exceptions)[inputs]: Remove ghc-stm. (ghc-case-insensitive)[inputs]: Remove ghc-text. (ghc-megaparsec)[inputs]: Same. (ghc-network-uri)[inputs]: Remove ghc-parsec. (ghc-monad-control)[inputs]: Remove ghc-stm. (ghc-blaze-builder)[inputs]: Remove ghc-text. (ghc-blaze-markup)[inputs]: Same. (ghc-async)[inputs]: Remove ghc-stm. (ghc-invariant)[inputs]: Same. (ghc-statevar)[inputs]: Same. (ghc-lens)[inputs]: Remove ghc-text. (ghc-cheapskate)[inputs]: Same. (ghc-semigroups)[inputs]: Same. (ghc-semigroups-bootstrap)[inputs]: Same. (ghc-fast-logger)[inputs]: Same. (ghc-scientific)[inputs]: Same. (ghc-scientific-bootstrap)[inputs]: Same. (ghc-texmath)[inputs]: Remove ghc-parsec. (ghc-highlighting-kate)[inputs]: Same. (ghc-cmark)[inputs]: Remove ghc-text. (ghc-cmark-gfm)[inputs]: Same. (ghc-th-lift-instances)[inputs]: Same. (ghc-yaml)[inputs]: Same. (ghc-hslua)[inputs]: Same. (ghc-hslua-module-text)[inputs]: Same. (ghc-skylighting-core)[inputs]: Same. (ghc-doctemplates)[inputs]: Remove ghc-text and ghc-parsec. (ghc-pandoc)[inputs]: Same. (ghc-typed-process)[inputs]: Remove ghc-stm. (ghc-conduit-extra)[inputs]: Remove ghc-stm and ghc-text. (ghc-xml-types)[inputs]: Remove ghc-text. (ghc-xml-conduit)[inputs]: Same. (ghc-pandoc-citeproc)[inputs]: Remove ghc-text and ghc-parsec. (ghc-regex-tdfa)[inputs]: Remove ghc-parsec. (ghc-wl-pprint-text)[inputs]: Remove ghc-text. (ghc-graphviz)[inputs]: Same. (ghc-system-filepath-bootstrap)[inputs]: Same. (ghc-system-fileio-bootstrap)[inputs]: Same. (ghc-shelly)[inputs]: Same. (ghc-chell)[inputs]: Same. (ghc-system-filepath)[inputs]: Same. (ghc-system-fileio)[inputs]: Same. (ghc-fsnotify)[inputs]: Same. (ghc-json)[inputs]: Remove ghc-text and ghc-parsec. (ghc-esqueleto)[inputs]: Remove ghc-text. (shellcheck)[inputs]: Remove ghc-parsec. (ghc-errors)[inputs]: Remove ghc-text. (ghc-chunked-data)[inputs]: Same. (ghc-uuid-types)[inputs]: Same. (ghc-uuid)[inputs]: Same. (ghc-rebase)[inputs]: Remove ghc-stm and ghc-text. (ghc-foldl)[inputs]: Remove ghc-text. (ghc-mono-traversable)[inputs]: Same. (ghc-conduit-combinators)[inputs]: Same. (ghc-aws)[inputs]: Same. (ghc-stm-chans)[inputs]: Remove ghc-stm. (ghc-monad-logger)[inputs]: Remove ghc-text and ghc-stm. (ghc-shakespeare)[inputs]: Remove ghc-parsec and ghc-text. (ghc-resource-pool)[inputs]: Remove ghc-stm. (ghc-attoparsec-iso8601)[inputs]: Remove ghc-text. (ghc-http-api-data)[inputs]: Same. (ghc-persistent)[inputs]: Same. (ghc-aeson-compat)[inputs]: Same. (ghc-persistent-template)[inputs]: Same. (ghc-unliftio)[inputs]: Remove ghc-stm. (ghc-persistent-sqlite)[native-inputs]: Remove ghc-text. (ghc-bytes)[inputs]: Same. (ghc-missingh)[inputs]: Remove ghc-parsec. (ghc-rio)[inputs]: Remove ghc-text. (ghc-cairo)[inputs]: Same. (ghc-atomic-write)[inputs]: Remove ghc-text. [native-inputs]: Same. (ghc-stm-conduit)[inputs]: Remove ghc-stm. (ghc-conduit-algorithms)[inputs]: Same. (ghc-interpolate)[native-inputs]: Remove ghc-text. (ghc-hpack)[inputs]: Same. (ghc-inline-c)[inputs]: Remove ghc-parsec. (ghc-configurator)[inputs]: Remove ghc-text. (ghc-c2hs)[native-inputs]: Same. (ghc-libmpd)[inputs]: Same. (ghc-concurrent-output)[inputs]: Remove ghc-stm. * gnu/packages/idris.scm (idris)[inputs]: Remove ghc-text. * gnu/packages/wm.scm (xmobar)[inputs]: Remove ghc-parsec and ghc-stm. Signed-off-by: Ricardo Wurmus --- gnu/packages/bioinformatics.scm | 2 -- 1 file changed, 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 956257d7bb..991a3c6487 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -13964,13 +13964,11 @@ datasets.") ("ghc-intervalmap" ,ghc-intervalmap) ("ghc-missingh" ,ghc-missingh) ("ghc-optparse-applicative" ,ghc-optparse-applicative) - ("ghc-parsec" ,ghc-parsec) ("ghc-regex" ,ghc-regex) ("ghc-safe" ,ghc-safe) ("ghc-safeio" ,ghc-safeio) ("ghc-strict" ,ghc-strict) ("ghc-tar" ,ghc-tar) - ("ghc-text" ,ghc-text) ("ghc-unliftio" ,ghc-unliftio) ("ghc-unliftio-core" ,ghc-unliftio-core) ("ghc-vector" ,ghc-vector) -- cgit v1.2.3 From 62a031afc438dcf2c2b38259334cb6e3b369a908 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:34 +0200 Subject: gnu: Add tabixpp. * gnu/packages/bioinformatics.scm (tabixpp): New variable. --- gnu/packages/bioinformatics.scm | 40 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 40 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 991a3c6487..5a63399967 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14827,3 +14827,43 @@ trees by inserting random mutations. The tbsp package implements an alternative method to detect significant, cell type specific sequence mutations from scRNA-Seq data.") (license license:expat)))) + +(define-public tabixpp + (package + (name "tabixpp") + (version "1.0.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/tabixpp") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "08vx6nsipk971cyr8z53rnzwkvlld63kcn1fw0pwddynz91xfny8")))) + (build-system gnu-build-system) + (inputs + `(("htslib" ,htslib) + ("zlib" ,zlib))) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + ;; The build phase needs overriding the location of htslib. + (replace 'build + (lambda* (#:key inputs #:allow-other-keys) + (let ((htslib-ref (assoc-ref inputs "htslib"))) + (invoke "make" + (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") + "HTS_HEADERS=" ; No need to check for headers here. + (string-append "LIBPATH=-L. -L" htslib-ref "/include"))))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (install-file "tabix++" bin)) + #t))))) + (home-page "https://github.com/ekg/tabixpp") + (synopsis "C++ wrapper around tabix project") + (description "This is a C++ wrapper around the Tabix project which abstracts +some of the details of opening and jumping in tabix-indexed files.") + (license license:expat))) -- cgit v1.2.3 From 7faa70cf2b6a81f2670b52e5caa502e409626faa Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:35 +0200 Subject: gnu: Add smithwaterman. * gnu/packages/bioinformatics.scm (smithwaterman): New variable. --- gnu/packages/bioinformatics.scm | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 5a63399967..2105393473 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14867,3 +14867,34 @@ mutations from scRNA-Seq data.") (description "This is a C++ wrapper around the Tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.") (license license:expat))) + +(define-public smithwaterman + ;; TODO: Upgrading smithwaterman breaks FreeBayes. + (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) + (package + (name "smithwaterman") + (version (string-append "0-1." (string-take commit 7))) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/smithwaterman/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0z9xsmsv452kgdfbbwydyc6nymg3fwyv8zswls8qjin3r4ia4415")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (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 "smithwaterman" bin)) + #t))))) + (home-page "https://github.com/ekg/smithwaterman") + (synopsis "Implementation of the Smith-Waterman algorithm") + (description "Implementation of the Smith-Waterman algorithm.") + ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9. + (license (list license:gpl2 license:expat))))) -- cgit v1.2.3 From 8cd51276e53fc4988029bcd2de2b69db68ea6e05 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:36 +0200 Subject: gnu: Add multichoose. * gnu/packages/bioinformatics.scm (multichoose): New variable. --- gnu/packages/bioinformatics.scm | 34 ++++++++++++++++++++++++++++++++++ 1 file changed, 34 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 2105393473..086e9324cb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14898,3 +14898,37 @@ some of the details of opening and jumping in tabix-indexed files.") (description "Implementation of the Smith-Waterman algorithm.") ;; The licensing terms are unclear: https://github.com/ekg/smithwaterman/issues/9. (license (list license:gpl2 license:expat))))) + +(define-public multichoose + (package + (name "multichoose") + (version "1.0.3") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/multichoose/") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0ci5fqvmpamwgxvmyd79ygj6n3bnbl3vc7b6h1sxz58186sm3pfs")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; Tests require node. + #:phases + (modify-phases %standard-phases + (delete 'configure) ; There is no configure phase. + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + ;; TODO: There are Python modules for these programs too. + (install-file "multichoose" bin) + (install-file "multipermute" bin)) + #t))))) + (home-page "https://github.com/ekg/multichoose") + (synopsis "Efficient loopless multiset combination generation algorithm") + (description "This library implements an efficient loopless multiset +combination generation algorithm which is (approximately) described in +\"Loopless algorithms for generating permutations, combinations, and other +combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM), +1973. (Algorithm 7.)") + (license license:expat))) -- cgit v1.2.3 From 70782dddffc2da05fed6aba35c3121a2265fd649 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:37 +0200 Subject: gnu: Add fsom. * gnu/packages/bioinformatics.scm (fsom): New variable. --- gnu/packages/bioinformatics.scm | 30 ++++++++++++++++++++++++++++++ 1 file changed, 30 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 086e9324cb..a3c83f73bb 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14932,3 +14932,33 @@ combination generation algorithm which is (approximately) described in combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM), 1973. (Algorithm 7.)") (license license:expat))) + +(define-public fsom + (let ((commit "a6ef318fbd347c53189384aef7f670c0e6ce89a3")) + (package + (name "fsom") + (version (git-version "0.0.0" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/fsom/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0gw1lpvr812pywg9y546x0h1hhj261xwls41r6kqhddjlrcjc0pi")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; There are no tests to run. + #:phases + (modify-phases %standard-phases + (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 "fsom" bin)) + #t))))) + (home-page "https://github.com/ekg/fsom") + (synopsis "Manage SOM (Self-Organizing Maps) neural networks") + (description "A tiny C library for managing SOM (Self-Organizing Maps) +neural networks.") + (license license:gpl3)))) -- cgit v1.2.3 From 7d71557d4d3ca5bdd33eb8c9bdf0cd2aba624554 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:38 +0200 Subject: gnu: Add fastahack. * gnu/packages/bioinformatics.scm (fastahack): New variable. --- gnu/packages/bioinformatics.scm | 33 +++++++++++++++++++++++++++++++++ 1 file changed, 33 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index a3c83f73bb..4dae22082d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14962,3 +14962,36 @@ combinatorial configurations.\", G. Ehrlich - Journal of the ACM (JACM), (description "A tiny C library for managing SOM (Self-Organizing Maps) neural networks.") (license license:gpl3)))) + +(define-public fastahack + (let ((commit "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd")) + (package + (name "fastahack") + (version (git-version "0.0.0" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/fastahack/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "0hfdv67l9g611i2ck4l92pd6ygmsp9g1ph4zx1ni7qkpsikf0l19")))) + (build-system gnu-build-system) + (arguments + `(#:tests? #f ; Unclear how to run tests: https://github.com/ekg/fastahack/issues/15 + #:phases + (modify-phases %standard-phases + (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 "fastahack" bin)) + #t))))) + (home-page "https://github.com/ekg/fastahack") + (synopsis "Indexing and sequence extraction from FASTA files") + (description "Fastahack is a small application for indexing and +extracting sequences and subsequences from FASTA files. The included library +provides a FASTA reader and indexer that can be embedded into applications +which would benefit from directly reading subsequences from FASTA files. The +library automatically handles index file generation and use.") + (license (list license:expat license:gpl2))))) -- cgit v1.2.3 From 194e45f90addf5f9bd3e7e2de1dd50b3071f053b Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:39 +0200 Subject: gnu: Add vcflib. * gnu/packages/bioinformatics.scm (vcflib): New variable. --- gnu/packages/bioinformatics.scm | 105 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 105 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4dae22082d..7808976a1f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14868,6 +14868,24 @@ mutations from scRNA-Seq data.") some of the details of opening and jumping in tabix-indexed files.") (license license:expat))) +(define tabixpp-freebayes + ;; This version works with FreeBayes while the released + ;; version doesn't. The released creates a variable with the name \"vcf\" + ;; somewhere, which is also the name of a namespace in vcflib. + (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7")) + (package + (inherit tabixpp) + (name "tabixpp-freebayes") + (version (git-version "0.0.0" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/tabixpp/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "017qsmsc2kyiyzqr9nl8cc6pfldxf16dbn8flx5i59mbqr9ydi7g"))))))) + (define-public smithwaterman ;; TODO: Upgrading smithwaterman breaks FreeBayes. (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) @@ -14995,3 +15013,90 @@ provides a FASTA reader and indexer that can be embedded into applications which would benefit from directly reading subsequences from FASTA files. The library automatically handles index file generation and use.") (license (list license:expat license:gpl2))))) + +(define-public vcflib + (let ((commit "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92") + (revision "1")) + (name "vcflib") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vcflib/vcflib/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1gijvcz1lcdn5kvgzb671l6iby0379qk00nqmcrszgk67hfwx6kq")))) + (build-system gnu-build-system) + (inputs + `(("zlib" ,zlib))) + (native-inputs + `(("perl" ,perl) + ("python" ,python-2) + ;; Submodules. + ;; This package builds against the .o files so we need to extract the source. + ("tabixpp-src" ,(package-source tabixpp-freebayes)) + ("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" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/intervaltree/") + (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838"))) + (file-name "intervaltree-src-checkout") + (sha256 + (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj")))))) + (arguments + `(#:tests? #f ; no tests + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'check) + (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 "intervaltree-src" "intervaltree") + (unpack "fastahack-src" "fastahack") + (unpack "filevercmp-src" "filevercmp") + (unpack "fsom-src" "fsom") + (unpack "multichoose-src" "multichoose") + (unpack "smithwaterman-src" "smithwaterman") + (unpack "tabixpp-src" "tabixpp"))))) + (replace 'build + (lambda* (#:key inputs make-flags #:allow-other-keys) + (with-directory-excursion "tabixpp" + (invoke "make")) + (invoke "make" "CC=gcc" + (string-append "CFLAGS=\"" "-Itabixpp " "\"") + "all"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin")) + (lib (string-append (assoc-ref outputs "out") "/lib"))) + (for-each (lambda (file) + (install-file file bin)) + (find-files "bin" ".*")) + ;; The header files in src/ do not interface libvcflib, + ;; therefore they are left out. + (install-file "libvcflib.a" lib)) + #t))))) + (home-page "https://github.com/vcflib/vcflib/") + (synopsis "Library for parsing and manipulating VCF files") + (description "Vcflib provides methods to manipulate and interpret +sequence variation as it can be described by VCF. It is both an API for parsing +and operating on records of genomic variation as it can be described by the VCF +format, and a collection of command-line utilities for executing complex +manipulations on VCF files.") + (license license:expat)))) -- cgit v1.2.3 From 173e046950e153477a6aaa0f4860d8f080df6843 Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:40 +0200 Subject: gnu: Add freebayes. * gnu/packages/bioinformatics.scm (freebayes): New variable. --- gnu/packages/bioinformatics.scm | 123 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 123 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7808976a1f..311a83e53b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15100,3 +15100,126 @@ and operating on records of genomic variation as it can be described by the VCF format, and a collection of command-line utilities for executing complex 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.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2")))) + (build-system gnu-build-system) + (inputs + `(("zlib" ,zlib) + ("htslib" ,htslib))) + (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. + ("bamtools" ,bamtools) + ("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-freebayes)) + ("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" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/intervaltree/") + (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838"))) + (file-name "intervaltree-src-checkout") + (sha256 + (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj")))) + ;; 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 + `(#:tests? #f ; TODO: Re-enable when we have grep with perl support. + #:test-target "test" + #:phases + (modify-phases %standard-phases + (delete 'configure) + (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-makefile + (lambda* (#:key inputs #:allow-other-keys) + ;; We don't have the .git folder to get the version tag from. + (substitute* '("vcflib/Makefile") + (("^GIT_VERSION.*") (string-append "GIT_VERSION = v" ,version))))) + (replace 'build + (lambda* (#:key inputs make-flags #:allow-other-keys) + (with-directory-excursion "vcflib" + (with-directory-excursion "tabixpp" + (pk "Compile tabixpp before compiling the main project.") + (let ((htslib-ref (assoc-ref inputs "htslib"))) + (invoke "make" "HTS_HEADERS=" + (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") + (string-append "LIBPATH=-L. -L" htslib-ref "/include")))) + (pk "Compile vcflib before compiling the main project.") + (invoke "make" "CC=gcc" + (string-append "CFLAGS=\"" "-Itabixpp " + "-I" (assoc-ref inputs "htslib") "/include " "\"") + "all")) + (pk "Compile the main project.") + (with-directory-excursion "src" + (substitute* "Makefile" + (("-I\\$\\(BAMTOOLS_ROOT\\)/src") "-I$(BAMTOOLS_ROOT)/include/bamtools")) + (invoke "make" + (string-append "BAMTOOLS_ROOT=" + (assoc-ref inputs "bamtools")))))) + (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 +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)))) -- cgit v1.2.3 From 6bc63fd8a7a44a3b2bd1686be619237e7dd94ef1 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 8 Aug 2019 15:32:39 +0300 Subject: Revert "gnu: Add freebayes." This reverts commit 173e046950e153477a6aaa0f4860d8f080df6843. --- gnu/packages/bioinformatics.scm | 123 ---------------------------------------- 1 file changed, 123 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 311a83e53b..7808976a1f 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15100,126 +15100,3 @@ and operating on records of genomic variation as it can be described by the VCF format, and a collection of command-line utilities for executing complex 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.git") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2")))) - (build-system gnu-build-system) - (inputs - `(("zlib" ,zlib) - ("htslib" ,htslib))) - (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. - ("bamtools" ,bamtools) - ("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-freebayes)) - ("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" - ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/intervaltree/") - (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838"))) - (file-name "intervaltree-src-checkout") - (sha256 - (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj")))) - ;; 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 - `(#:tests? #f ; TODO: Re-enable when we have grep with perl support. - #:test-target "test" - #:phases - (modify-phases %standard-phases - (delete 'configure) - (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-makefile - (lambda* (#:key inputs #:allow-other-keys) - ;; We don't have the .git folder to get the version tag from. - (substitute* '("vcflib/Makefile") - (("^GIT_VERSION.*") (string-append "GIT_VERSION = v" ,version))))) - (replace 'build - (lambda* (#:key inputs make-flags #:allow-other-keys) - (with-directory-excursion "vcflib" - (with-directory-excursion "tabixpp" - (pk "Compile tabixpp before compiling the main project.") - (let ((htslib-ref (assoc-ref inputs "htslib"))) - (invoke "make" "HTS_HEADERS=" - (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") - (string-append "LIBPATH=-L. -L" htslib-ref "/include")))) - (pk "Compile vcflib before compiling the main project.") - (invoke "make" "CC=gcc" - (string-append "CFLAGS=\"" "-Itabixpp " - "-I" (assoc-ref inputs "htslib") "/include " "\"") - "all")) - (pk "Compile the main project.") - (with-directory-excursion "src" - (substitute* "Makefile" - (("-I\\$\\(BAMTOOLS_ROOT\\)/src") "-I$(BAMTOOLS_ROOT)/include/bamtools")) - (invoke "make" - (string-append "BAMTOOLS_ROOT=" - (assoc-ref inputs "bamtools")))))) - (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 -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)))) -- cgit v1.2.3 From 1a069a170c636751695d54c2b282a196eda773c6 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Thu, 8 Aug 2019 15:33:37 +0300 Subject: Revert "gnu: Add vcflib." This reverts commit 194e45f90addf5f9bd3e7e2de1dd50b3071f053b. This commit does not have a good commit message, and it breaks master --- gnu/packages/bioinformatics.scm | 105 ---------------------------------------- 1 file changed, 105 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7808976a1f..4dae22082d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14868,24 +14868,6 @@ mutations from scRNA-Seq data.") some of the details of opening and jumping in tabix-indexed files.") (license license:expat))) -(define tabixpp-freebayes - ;; This version works with FreeBayes while the released - ;; version doesn't. The released creates a variable with the name \"vcf\" - ;; somewhere, which is also the name of a namespace in vcflib. - (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7")) - (package - (inherit tabixpp) - (name "tabixpp-freebayes") - (version (git-version "0.0.0" "1" commit)) - (source (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/tabixpp/") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "017qsmsc2kyiyzqr9nl8cc6pfldxf16dbn8flx5i59mbqr9ydi7g"))))))) - (define-public smithwaterman ;; TODO: Upgrading smithwaterman breaks FreeBayes. (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) @@ -15013,90 +14995,3 @@ provides a FASTA reader and indexer that can be embedded into applications which would benefit from directly reading subsequences from FASTA files. The library automatically handles index file generation and use.") (license (list license:expat license:gpl2))))) - -(define-public vcflib - (let ((commit "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92") - (revision "1")) - (name "vcflib") - (version (git-version "0.0.0" revision commit)) - (source - (origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/vcflib/vcflib/") - (commit commit))) - (file-name (git-file-name name version)) - (sha256 - (base32 "1gijvcz1lcdn5kvgzb671l6iby0379qk00nqmcrszgk67hfwx6kq")))) - (build-system gnu-build-system) - (inputs - `(("zlib" ,zlib))) - (native-inputs - `(("perl" ,perl) - ("python" ,python-2) - ;; Submodules. - ;; This package builds against the .o files so we need to extract the source. - ("tabixpp-src" ,(package-source tabixpp-freebayes)) - ("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" - ,(origin - (method git-fetch) - (uri (git-reference - (url "https://github.com/ekg/intervaltree/") - (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838"))) - (file-name "intervaltree-src-checkout") - (sha256 - (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj")))))) - (arguments - `(#:tests? #f ; no tests - #:phases - (modify-phases %standard-phases - (delete 'configure) - (delete 'check) - (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 "intervaltree-src" "intervaltree") - (unpack "fastahack-src" "fastahack") - (unpack "filevercmp-src" "filevercmp") - (unpack "fsom-src" "fsom") - (unpack "multichoose-src" "multichoose") - (unpack "smithwaterman-src" "smithwaterman") - (unpack "tabixpp-src" "tabixpp"))))) - (replace 'build - (lambda* (#:key inputs make-flags #:allow-other-keys) - (with-directory-excursion "tabixpp" - (invoke "make")) - (invoke "make" "CC=gcc" - (string-append "CFLAGS=\"" "-Itabixpp " "\"") - "all"))) - (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin")) - (lib (string-append (assoc-ref outputs "out") "/lib"))) - (for-each (lambda (file) - (install-file file bin)) - (find-files "bin" ".*")) - ;; The header files in src/ do not interface libvcflib, - ;; therefore they are left out. - (install-file "libvcflib.a" lib)) - #t))))) - (home-page "https://github.com/vcflib/vcflib/") - (synopsis "Library for parsing and manipulating VCF files") - (description "Vcflib provides methods to manipulate and interpret -sequence variation as it can be described by VCF. It is both an API for parsing -and operating on records of genomic variation as it can be described by the VCF -format, and a collection of command-line utilities for executing complex -manipulations on VCF files.") - (license license:expat)))) -- cgit v1.2.3 From a39f2e4cea3954497b541eba71e24627ce111b15 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Aug 2019 16:35:00 +0200 Subject: gnu: r-biocparallel: Update to 1.18.1. * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.18.1. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 4dae22082d..1bf9278c5d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7691,13 +7691,13 @@ powerful online queries from gene annotation to database mining.") (define-public r-biocparallel (package (name "r-biocparallel") - (version "1.18.0") + (version "1.18.1") (source (origin (method url-fetch) (uri (bioconductor-uri "BiocParallel" version)) (sha256 (base32 - "0v8rhf3hbgb3v32h2pmsv1y6q2x4airmpp50fk7z6ardcn4aza7x")))) + "1j6wbls4qgvi5gj99c51r00jhxrzxk3x3258wg7dcjzbfqypvyw3")))) (properties `((upstream-name . "BiocParallel"))) (build-system r-build-system) -- cgit v1.2.3 From 90060e2071cf3c21430d6470d15324c502bccc4c Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 8 Aug 2019 16:35:07 +0200 Subject: gnu: r-hdf5array: Update to 1.12.2. * gnu/packages/bioinformatics.scm (r-hdf5array): Update to 1.12.2. --- gnu/packages/bioinformatics.scm | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 1bf9278c5d..e860b5b881 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10425,14 +10425,14 @@ provided.") (define-public r-hdf5array (package (name "r-hdf5array") - (version "1.12.1") + (version "1.12.2") (source (origin (method url-fetch) (uri (bioconductor-uri "HDF5Array" version)) (sha256 (base32 - "0n8zc1x582vwb0zfhrjmnqbnpqky9zbhjc2j836i0a4yisklwdcp")))) + "0afradisrr5gn0lf2kxjw55vdm3lm9mlgx53qlr9r40c1hrydpf5")))) (properties `((upstream-name . "HDF5Array"))) (build-system r-build-system) (inputs -- cgit v1.2.3 From 95fb1a185106d1a5dcfb035ba62c28e0fd9fb80a Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:39 +0200 Subject: gnu: Add vcflib. * gnu/packages/bioinformatics.scm (vcflib): New variable. (tabixpp-freebayes): New private variable. --- gnu/packages/bioinformatics.scm | 106 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 106 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e860b5b881..99648d6b74 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -14868,6 +14868,24 @@ mutations from scRNA-Seq data.") some of the details of opening and jumping in tabix-indexed files.") (license license:expat))) +(define tabixpp-freebayes + ;; This version works with FreeBayes while the released + ;; version doesn't. The released creates a variable with the name \"vcf\" + ;; somewhere, which is also the name of a namespace in vcflib. + (let ((commit "bbc63a49acc52212199f92e9e3b8fba0a593e3f7")) + (package + (inherit tabixpp) + (name "tabixpp-freebayes") + (version (git-version "0.0.0" "1" commit)) + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/tabixpp/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "017qsmsc2kyiyzqr9nl8cc6pfldxf16dbn8flx5i59mbqr9ydi7g"))))))) + (define-public smithwaterman ;; TODO: Upgrading smithwaterman breaks FreeBayes. (let ((commit "203218b47d45ac56ef234716f1bd4c741b289be1")) @@ -14995,3 +15013,91 @@ provides a FASTA reader and indexer that can be embedded into applications which would benefit from directly reading subsequences from FASTA files. The library automatically handles index file generation and use.") (license (list license:expat license:gpl2))))) + +(define-public vcflib + (let ((commit "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92") + (revision "1")) + (package + (name "vcflib") + (version (git-version "0.0.0" revision commit)) + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vcflib/vcflib/") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1gijvcz1lcdn5kvgzb671l6iby0379qk00nqmcrszgk67hfwx6kq")))) + (build-system gnu-build-system) + (inputs + `(("zlib" ,zlib))) + (native-inputs + `(("perl" ,perl) + ("python" ,python-2) + ;; Submodules. + ;; This package builds against the .o files so we need to extract the source. + ("tabixpp-src" ,(package-source tabixpp-freebayes)) + ("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" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/intervaltree/") + (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838"))) + (file-name "intervaltree-src-checkout") + (sha256 + (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj")))))) + (arguments + `(#:tests? #f ; no tests + #:phases + (modify-phases %standard-phases + (delete 'configure) + (delete 'check) + (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 "intervaltree-src" "intervaltree") + (unpack "fastahack-src" "fastahack") + (unpack "filevercmp-src" "filevercmp") + (unpack "fsom-src" "fsom") + (unpack "multichoose-src" "multichoose") + (unpack "smithwaterman-src" "smithwaterman") + (unpack "tabixpp-src" "tabixpp"))))) + (replace 'build + (lambda* (#:key inputs make-flags #:allow-other-keys) + (with-directory-excursion "tabixpp" + (invoke "make")) + (invoke "make" "CC=gcc" + (string-append "CFLAGS=\"" "-Itabixpp " "\"") + "all"))) + (replace 'install + (lambda* (#:key outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin")) + (lib (string-append (assoc-ref outputs "out") "/lib"))) + (for-each (lambda (file) + (install-file file bin)) + (find-files "bin" ".*")) + ;; The header files in src/ do not interface libvcflib, + ;; therefore they are left out. + (install-file "libvcflib.a" lib)) + #t))))) + (home-page "https://github.com/vcflib/vcflib/") + (synopsis "Library for parsing and manipulating VCF files") + (description "Vcflib provides methods to manipulate and interpret +sequence variation as it can be described by VCF. It is both an API for parsing +and operating on records of genomic variation as it can be described by the VCF +format, and a collection of command-line utilities for executing complex +manipulations on VCF files.") + (license license:expat)))) -- cgit v1.2.3 From 8803dbdad80aaf5a67ace81e3b6a336efee3c60d Mon Sep 17 00:00:00 2001 From: Pierre Neidhardt Date: Sat, 18 May 2019 19:26:40 +0200 Subject: gnu: Add freebayes. * gnu/packages/bioinformatics.scm (freebayes): New variable. --- gnu/packages/bioinformatics.scm | 123 ++++++++++++++++++++++++++++++++++++++++ 1 file changed, 123 insertions(+) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 99648d6b74..f6a3b8422b 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15101,3 +15101,126 @@ and operating on records of genomic variation as it can be described by the VCF format, and a collection of command-line utilities for executing complex 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.git") + (commit commit))) + (file-name (git-file-name name version)) + (sha256 + (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2")))) + (build-system gnu-build-system) + (inputs + `(("zlib" ,zlib) + ("htslib" ,htslib))) + (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. + ("bamtools" ,bamtools) + ("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-freebayes)) + ("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" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/ekg/intervaltree/") + (commit "dbb4c513d1ad3baac516fc1484c995daf9b42838"))) + (file-name "intervaltree-src-checkout") + (sha256 + (base32 "1fy5qbj4bg8d2bjysvaa9wfnqn2rj2sk5yra2h4l5pzvy53f23fj")))) + ;; 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 + `(#:tests? #f ; TODO: Re-enable when we have grep with perl support. + #:test-target "test" + #:phases + (modify-phases %standard-phases + (delete 'configure) + (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-makefile + (lambda* (#:key inputs #:allow-other-keys) + ;; We don't have the .git folder to get the version tag from. + (substitute* '("vcflib/Makefile") + (("^GIT_VERSION.*") (string-append "GIT_VERSION = v" ,version))))) + (replace 'build + (lambda* (#:key inputs make-flags #:allow-other-keys) + (with-directory-excursion "vcflib" + (with-directory-excursion "tabixpp" + (pk "Compile tabixpp before compiling the main project.") + (let ((htslib-ref (assoc-ref inputs "htslib"))) + (invoke "make" "HTS_HEADERS=" + (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") + (string-append "LIBPATH=-L. -L" htslib-ref "/include")))) + (pk "Compile vcflib before compiling the main project.") + (invoke "make" "CC=gcc" + (string-append "CFLAGS=\"" "-Itabixpp " + "-I" (assoc-ref inputs "htslib") "/include " "\"") + "all")) + (pk "Compile the main project.") + (with-directory-excursion "src" + (substitute* "Makefile" + (("-I\\$\\(BAMTOOLS_ROOT\\)/src") "-I$(BAMTOOLS_ROOT)/include/bamtools")) + (invoke "make" + (string-append "BAMTOOLS_ROOT=" + (assoc-ref inputs "bamtools")))))) + (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 +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)))) -- cgit v1.2.3 From 7cd98e868ed00898cff5ac3749194b2b42fc02bb Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 9 Aug 2019 12:03:14 +0200 Subject: gnu: freebayes: Move bamtools to inputs. * gnu/packages/bioinformatics.scm (freebayes)[native-inputs]: Move bamtools from here... [inputs]: ...to here. --- gnu/packages/bioinformatics.scm | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index f6a3b8422b..3f1e6b3188 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15119,8 +15119,9 @@ manipulations on VCF files.") (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2")))) (build-system gnu-build-system) (inputs - `(("zlib" ,zlib) - ("htslib" ,htslib))) + `(("bamtools" ,bamtools) + ("htslib" ,htslib) + ("zlib" ,zlib))) (native-inputs `(("bc" ,bc) ; Needed for running tests. ("samtools" ,samtools) ; Needed for running tests. @@ -15128,7 +15129,6 @@ manipulations on VCF files.") ("perl" ,perl) ; Needed for running tests. ("procps" ,procps) ; Needed for running tests. ("python" ,python-2) ; Needed for running tests. - ("bamtools" ,bamtools) ("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. -- cgit v1.2.3 From c2847323d8e1be6259c18a5026f5af9c9eec598b Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Fri, 9 Aug 2019 12:06:59 +0200 Subject: gnu: freebayes: Simplify and enable tests. * gnu/packages/bioinformatics.scm (freebayes)[arguments]: Enable tests; set make flags; add phase "fix-tests"; fix both Makefiles in "fix-makefiles" phase; move build of tabixpp and vcflib to separate phase "build-tabixpp-and-vcflib"; simplify make invocations; remove custom "build" phase. --- gnu/packages/bioinformatics.scm | 52 +++++++++++++++++++++++------------------ 1 file changed, 29 insertions(+), 23 deletions(-) (limited to 'gnu/packages/bioinformatics.scm') diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3f1e6b3188..a9e0264369 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -15159,11 +15159,20 @@ manipulations on VCF files.") (sha256 (base32 "043plp6z0x9yf7mdpky1fw7zcpwn1p47px95w9mh16603zqqqpga")))))) (arguments - `(#:tests? #f ; TODO: Re-enable when we have grep with perl support. + `(#: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)$'")) + #t)) (add-after 'unpack 'unpack-submodule-sources (lambda* (#:key inputs #:allow-other-keys) (let ((unpack (lambda (source target) @@ -15184,32 +15193,29 @@ manipulations on VCF files.") (unpack "tabixpp-src" "vcflib/tabixpp") (unpack "test-simple-bash-src" "test/test-simple-bash") (unpack "bash-tap-src" "test/bash-tap"))))) - (add-after 'unpack-submodule-sources 'fix-makefile - (lambda* (#:key inputs #:allow-other-keys) + (add-after 'unpack-submodule-sources 'fix-makefiles + (lambda _ ;; We don't have the .git folder to get the version tag from. - (substitute* '("vcflib/Makefile") - (("^GIT_VERSION.*") (string-append "GIT_VERSION = v" ,version))))) - (replace 'build + (substitute* "vcflib/Makefile" + (("^GIT_VERSION.*") + (string-append "GIT_VERSION = v" ,version))) + (substitute* "src/Makefile" + (("-I\\$\\(BAMTOOLS_ROOT\\)/src") + "-I$(BAMTOOLS_ROOT)/include/bamtools")) + #t)) + (add-before 'build 'build-tabixpp-and-vcflib (lambda* (#:key inputs make-flags #:allow-other-keys) (with-directory-excursion "vcflib" (with-directory-excursion "tabixpp" - (pk "Compile tabixpp before compiling the main project.") - (let ((htslib-ref (assoc-ref inputs "htslib"))) - (invoke "make" "HTS_HEADERS=" - (string-append "HTS_LIB=" htslib-ref "/lib/libhts.a") - (string-append "LIBPATH=-L. -L" htslib-ref "/include")))) - (pk "Compile vcflib before compiling the main project.") - (invoke "make" "CC=gcc" - (string-append "CFLAGS=\"" "-Itabixpp " - "-I" (assoc-ref inputs "htslib") "/include " "\"") - "all")) - (pk "Compile the main project.") - (with-directory-excursion "src" - (substitute* "Makefile" - (("-I\\$\\(BAMTOOLS_ROOT\\)/src") "-I$(BAMTOOLS_ROOT)/include/bamtools")) - (invoke "make" - (string-append "BAMTOOLS_ROOT=" - (assoc-ref inputs "bamtools")))))) + (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"))) -- cgit v1.2.3