diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 27 |
1 files changed, 21 insertions, 6 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index d3d9344322..0e9c20f1f1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7,7 +7,7 @@ ;;; Copyright © 2016, 2017 Efraim Flashner <efraim@flashner.co.il> ;;; Copyright © 2016 Marius Bakke <mbakke@fastmail.com> ;;; Copyright © 2016 Raoul Bonnal <ilpuccio.febo@gmail.com> -;;; Copyright © 2017 Tobias Geerinckx-Rice <me@tobias.gr> +;;; Copyright © 2017, 2018 Tobias Geerinckx-Rice <me@tobias.gr> ;;; Copyright © 2017 Arun Isaac <arunisaac@systemreboot.net> ;;; ;;; This file is part of GNU Guix. @@ -493,6 +493,20 @@ BED, GFF/GTF, VCF.") (base32 "0ykjbps1y3z3085q94npw8i9x5gldc6shy8vlc08v76zljsm07hv")))) (build-system gnu-build-system) + (arguments + `(#:phases + (modify-phases %standard-phases + (add-after 'install 'wrap-executables + (lambda* (#:key inputs outputs #:allow-other-keys) + (let* ((out (assoc-ref outputs "out"))) + (for-each + (lambda (script) + (wrap-program (string-append out "/bin/" script) + `("R_LIBS_SITE" ":" = (,(getenv "R_LIBS_SITE"))))) + '("create_annotations_files.bash" + "create_metaplots.bash" + "Ribotaper_ORF_find.sh" + "Ribotaper.sh")))))))) (inputs `(("bedtools" ,bedtools-2.18) ("samtools" ,samtools-0.1) @@ -1439,7 +1453,7 @@ multiple sequence alignments.") (define-public python-pysam (package (name "python-pysam") - (version "0.11.2.2") + (version "0.13.0") (source (origin (method url-fetch) ;; Test data is missing on PyPi. @@ -1449,7 +1463,7 @@ multiple sequence alignments.") (file-name (string-append name "-" version ".tar.gz")) (sha256 (base32 - "1cfqdxsqs3xhacns9n0271ck6wkc76px66ddjm91wfw2jxxfklvc")) + "0dzap2axin9cbbl0d825w294bpn00zagfm1sigamm4v2pm5bj9lp")) (modules '((guix build utils))) (snippet ;; Drop bundled htslib. TODO: Also remove samtools and bcftools. @@ -3213,7 +3227,7 @@ VCF.") (define-public htslib (package (name "htslib") - (version "1.5") + (version "1.6") (source (origin (method url-fetch) (uri (string-append @@ -3221,7 +3235,7 @@ VCF.") version "/htslib-" version ".tar.bz2")) (sha256 (base32 - "0bcjmnbwp2bib1z1bkrp95w9v2syzdwdfqww10mkb1hxlmg52ax0")))) + "1jsca3hg4rbr6iqq6imkj4lsvgl8g9768bcmny3hlff2w25vx24m")))) (build-system gnu-build-system) (arguments `(#:phases @@ -3242,7 +3256,8 @@ VCF.") (synopsis "C library for reading/writing high-throughput sequencing data") (description "HTSlib is a C library for reading/writing high-throughput sequencing -data. It also provides the bgzip, htsfile, and tabix utilities.") +data. It also provides the @command{bgzip}, @command{htsfile}, and +@command{tabix} utilities.") ;; Files under cram/ are released under the modified BSD license; ;; the rest is released under the Expat license (license (list license:expat license:bsd-3)))) |