diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 105 |
1 files changed, 66 insertions, 39 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3db67f5427..82cd1e420d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4,7 +4,7 @@ ;;; Copyright © 2015, 2016 Pjotr Prins <pjotr.guix@thebird.nl> ;;; Copyright © 2015 Andreas Enge <andreas@enge.fr> ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> -;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il> +;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com> ;;; @@ -99,7 +99,7 @@ #: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 r-ape (package @@ -956,7 +956,7 @@ package provides command line tools using the Bio++ library.") (define-public blast+ (package (name "blast+") - (version "2.4.0") + (version "2.6.0") (source (origin (method url-fetch) (uri (string-append @@ -964,13 +964,15 @@ package provides command line tools using the Bio++ library.") version "/ncbi-blast-" version "+-src.tar.gz")) (sha256 (base32 - "14n9jik6vhiwjd3m7bach4xj1pzfn0szbsbyfxybd9l9cc43b6mb")) + "15n937pw5aqmyfjb6l387d18grqbb96l63d5xj4l7yyh0zbf2405")) + (patches (search-patches "blast+-fix-makefile.patch")) (modules '((guix build utils))) (snippet '(begin - ;; Remove bundled bzip2 and zlib + ;; Remove bundled bzip2, zlib and pcre. (delete-file-recursively "c++/src/util/compress/bzip2") (delete-file-recursively "c++/src/util/compress/zlib") + (delete-file-recursively "c++/src/util/regexp") (substitute* "c++/src/util/compress/Makefile.in" (("bzip2 zlib api") "api")) ;; Remove useless msbuild directory @@ -979,9 +981,8 @@ package provides command line tools using the Bio++ library.") #t)))) (build-system gnu-build-system) (arguments - `(;; There are three(!) tests for this massive library, and all fail with + `(;; There are two(!) tests for this massive library, and both fail with ;; "unparsable timing stats". - ;; ERR [127] -- [util/regexp] test_pcre.sh (unparsable timing stats) ;; ERR [127] -- [serial/datatool] datatool.sh (unparsable timing stats) ;; ERR [127] -- [serial/datatool] datatool_xml.sh (unparsable timing stats) #:tests? #f @@ -1014,6 +1015,7 @@ package provides command line tools using the Bio++ library.") ;; Rewrite hardcoded paths to various tools (substitute* (append '("src/build-system/configure.ac" "src/build-system/configure" + "src/build-system/helpers/run_with_lock.c" "scripts/common/impl/if_diff.sh" "scripts/common/impl/run_with_lock.sh" "src/build-system/Makefile.configurables.real" @@ -1062,17 +1064,22 @@ package provides command line tools using the Bio++ library.") (assoc-ref inputs "bzip2")) (string-append "--with-z=" (assoc-ref inputs "zlib")) + (string-append "--with-pcre=" + (assoc-ref inputs "pcre")) ;; Each library is built twice by default, once ;; with "-static" in its name, and again ;; without. "--without-static" "--with-dll")))))))) - (outputs '("out" ; 19 MB - "lib" ; 203 MB - "include")) ; 32 MB + (outputs '("out" ; 21 MB + "lib" ; 226 MB + "include")) ; 33 MB (inputs `(("bzip2" ,bzip2) - ("zlib" ,zlib))) + ("zlib" ,zlib) + ("pcre" ,pcre) + ("perl" ,perl) + ("python" ,python-wrapper))) (native-inputs `(("cpio" ,cpio))) (home-page "http://blast.ncbi.nlm.nih.gov") @@ -1309,14 +1316,14 @@ splice junctions between exons.") (define-public bwa (package (name "bwa") - (version "0.7.12") + (version "0.7.15") (source (origin (method url-fetch) (uri (string-append "mirror://sourceforge/bio-bwa/bwa-" version ".tar.bz2")) (sha256 (base32 - "1330dpqncv0px3pbhjzz1gwgg39kkcv2r9qp2xs0sixf8z8wl7bh")))) + "0585ikg0gv0mpyw9iq0bq9n0hr95867bbv8jbzs9pk4slkpsymig")))) (build-system gnu-build-system) (arguments '(#:tests? #f ;no "check" target @@ -1562,15 +1569,16 @@ high-throughput sequencing data – with an emphasis on simplicity.") (define-public cd-hit (package (name "cd-hit") - (version "4.6.6") + (version "4.6.8") (source (origin (method url-fetch) (uri (string-append "https://github.com/weizhongli/cdhit" "/releases/download/V" version - "/cd-hit-v" version "-2016-0711.tar.gz")) + "/cd-hit-v" version + "-2017-0621-source.tar.gz")) (sha256 (base32 - "1w8hd4fszgg29nqiz569fldwy012la77nljcmlhglgicws56z54p")))) + "1386dg2npx8p62wmv08mjzsd2z3waknb9j1gg3gkvblcy57hymnn")))) (build-system gnu-build-system) (arguments `(#:tests? #f ; there are no tests @@ -1590,7 +1598,7 @@ high-throughput sequencing data – with an emphasis on simplicity.") (("__DATE__") "\"0\"") (("\", %s, \" __TIME__ \"\\\\n\", date") "")) #t)) - ;; The "install" target does not create the target directory + ;; The "install" target does not create the target directory. (add-before 'install 'create-target-dir (lambda* (#:key outputs #:allow-other-keys) (mkdir-p (string-append (assoc-ref outputs "out") "/bin")) @@ -2050,11 +2058,29 @@ trees (phylogenies) and characters.") (native-inputs `(("python2-nose" ,python2-nose) ,@(package-native-inputs base)))))) +(define-public python-py2bit + (package + (name "python-py2bit") + (version "0.2.1") + (source + (origin + (method url-fetch) + (uri (pypi-uri "py2bit" version)) + (sha256 + (base32 + "1cdf4qlmgwsh1f4k0wdv2sr8x9qn4366p0k3614vbd0fpqiarxrl")))) + (build-system python-build-system) + (home-page "https://github.com/dpryan79/py2bit") + (synopsis "Access 2bit files using lib2bit") + (description + "This package provides Python bindings for lib2bit to access 2bit files +with Python.") + (license license:expat))) (define-public deeptools (package (name "deeptools") - (version "2.1.1") + (version "2.5.1") (source (origin (method url-fetch) (uri (string-append "https://github.com/fidelram/deepTools/" @@ -2062,22 +2088,20 @@ trees (phylogenies) and characters.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1nmfin0zjdby3vay3r4flvz94dr6qjhj41ax4yz3vx13j6wz8izd")))) + "1q8i12l2gvk4n2s8lhyzwhh9g4qbc8lrk5l7maz00yvd5g6z5540")))) (build-system python-build-system) - (arguments - `(#:python ,python-2)) (inputs - `(("python-scipy" ,python2-scipy) - ("python-numpy" ,python2-numpy) - ("python-numpydoc" ,python2-numpydoc) - ("python-matplotlib" ,python2-matplotlib) - ("python-bx-python" ,python2-bx-python) - ("python-pysam" ,python2-pysam) - ("python-pybigwig" ,python2-pybigwig))) + `(("python-scipy" ,python-scipy) + ("python-numpy" ,python-numpy) + ("python-numpydoc" ,python-numpydoc) + ("python-matplotlib" ,python-matplotlib) + ("python-pysam" ,python-pysam) + ("python-py2bit" ,python-py2bit) + ("python-pybigwig" ,python-pybigwig))) (native-inputs - `(("python-mock" ,python2-mock) ;for tests - ("python-nose" ,python2-nose) ;for tests - ("python-pytz" ,python2-pytz))) ;for tests + `(("python-mock" ,python-mock) ;for tests + ("python-nose" ,python-nose) ;for tests + ("python-pytz" ,python-pytz))) ;for tests (home-page "https://github.com/fidelram/deepTools") (synopsis "Tools for normalizing and visualizing deep-sequencing data") (description @@ -2094,7 +2118,7 @@ identify enrichments with functional annotations of the genome.") (define-public diamond (package (name "diamond") - (version "0.9.8") + (version "0.9.9") (source (origin (method url-fetch) (uri (string-append @@ -2103,7 +2127,7 @@ identify enrichments with functional annotations of the genome.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "04f501vj3i95i2b4n60831k00ljalifrq33419bbz0y3sjlmcnj3")))) + "04i03046g3l2vk9722z47r1p7j415g97vvz6d76ywmbawyiihcb1")))) (build-system cmake-build-system) (arguments '(#:tests? #f ; no "check" target @@ -2711,7 +2735,8 @@ comment or quality sections.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222")))) + "055ynn16gd12pf78n4vr2a9jlwsbwzajpdnf2y2yilg1krfff222")) + (patches (search-patches "gemma-intel-compat.patch")))) (inputs `(("gsl" ,gsl) ("lapack" ,lapack) @@ -2719,11 +2744,13 @@ comment or quality sections.") (build-system gnu-build-system) (arguments `(#:make-flags - '(,@(if (any (cute string-prefix? <> (or (%current-system) - (%current-target-system))) - '("x86_64" "mips64el" "aarch64")) - '("FORCE_DYNAMIC=1") ; use shared libs - '("FORCE_DYNAMIC=1" "FORCE_32BIT=1"))) + '(,@(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 (modify-phases %standard-phases (delete 'configure) |