diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 20 |
1 files changed, 13 insertions, 7 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 9bf629947b..e87cef61be 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -10,6 +10,7 @@ ;;; 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> ;;; ;;; This file is part of GNU Guix. ;;; @@ -3240,12 +3241,16 @@ VCF.") (msg (format #f "\ Class-Path: /~a \ - ~a/share/java/htsjdk.jar${line.separator}" + ~a/share/java/htsjdk.jar${line.separator}${line.separator}" ;; maximum line length is 70 (string-tabulate (const #\b) 57) (assoc-ref inputs "java-htsjdk")))) (if (member "manifest" name) `(,tag ,@kids + (replaceregexp + (@ (file "${manifest.file}") + (match "\\r\\n\\r\\n") + (replace "${line.separator}"))) (echo (@ (message ,msg) (file "${manifest.file}") @@ -3760,13 +3765,13 @@ experiments.") (define-public macs (package (name "macs") - (version "2.1.0.20151222") + (version "2.1.1.20160309") (source (origin (method url-fetch) (uri (pypi-uri "MACS2" version)) (sha256 (base32 - "1r2hcz6irhcq7lwbafjks98jbn34hv05avgbdjnp6w6mlfjkf8x5")))) + "09ixspd1vcqmz1c81ih70xs4m7qml2iy5vyx1y74zww3iy1vl210")))) (build-system python-build-system) (arguments `(#:python ,python-2 ; only compatible with Python 2.7 @@ -12828,11 +12833,12 @@ once. This package provides tools to perform Drop-seq analyses.") (lambda _ (substitute* "Makefile.in" (("(^ tests/test_trim_galore/test.sh).*" _ m) m) + (("^ tests/test_multiqc/test.sh") "") (("^ test.sh") "")) #t))))) (inputs `(("gzip" ,gzip) - ("snakemake" ,snakemake) + ("snakemake" ,snakemake-4) ("fastqc" ,fastqc) ("multiqc" ,multiqc) ("star" ,star) @@ -12926,7 +12932,7 @@ expression report comparing samples in an easily configurable manner.") ("fastqc" ,fastqc) ("bowtie" ,bowtie) ("idr" ,idr) - ("snakemake" ,snakemake) + ("snakemake" ,snakemake-4) ("samtools" ,samtools) ("bedtools" ,bedtools) ("kentutils" ,kentutils))) @@ -12987,7 +12993,7 @@ in an easily configurable manner.") ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) ("python-wrapper" ,python-wrapper) ("python-pyyaml" ,python-pyyaml) - ("snakemake" ,snakemake) + ("snakemake" ,snakemake-4) ("bismark" ,bismark) ("fastqc" ,fastqc) ("bowtie" ,bowtie) @@ -13036,7 +13042,7 @@ methylation and segmentation.") ("python-loompy" ,python-loompy) ("ghc-pandoc" ,ghc-pandoc-1) ("ghc-pandoc-citeproc" ,ghc-pandoc-citeproc-with-pandoc-1) - ("snakemake" ,snakemake) + ("snakemake" ,snakemake-4) ("star" ,star) ("r-minimal" ,r-minimal) ("r-argparser" ,r-argparser) |