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| -rw-r--r-- | gn/packages/bioinformatics.scm | 50 |
1 files changed, 50 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 628e656..94e1839 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -490,3 +490,53 @@ and BAM files. Current parallelised functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.") (license license:gpl2+))) + +(define-public picard + (package + (name "picard") + (version "2.1.0") + (source + (origin + (method url-fetch) + (uri (string-append + "https://github.com/broadinstitute/picard/archive/" + version ".tar.gz")) + (sha256 + (base32 "")))) + (home-page "http://broadinstitute.github.io/picard/") + (synopsis "A set of Java command line tools for manipulating high-throughput +sequencing data (HTS) data and formats") + (description "Picard comprises Java-based command-line utilities that +manipulate SAM files, and a Java API (HTSJDK) for creating new programs that +read and write SAM files. Both SAM text format and SAM binary (BAM) format are +supported.") + ;; The license is MIT. + (license license:expat) +)) + +(define-public fastqc + (package + (name "fastqc") + (version "0.11.4") + (source + (origin + (method url-fetch) + (uri (string-append + "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v" + version "_source.zip")) + (sha256 + (base32 "")))) + (build-system gnu-build-system) + (arguments + `(("perl" ,perl) ; Needed to run the java command. + ("jdk" ,icedtea "jdk"))) + (native-inputs + `(("ant" ,ant) ; TODO: Most Java packages need Ant, but in this case, IDK.. + ("jdk" ,icedtea "jdk") + ;;("htsjdk" ,htsjdk) ; It is based on htsjdk, but it ships its own copy. + ("unzip" ,unzip))) + (home-page "http://www.bioinformatics.babraham.ac.uk/projects/fastqc/") + (synopsis "A quality control tool for high throughput sequence data") + (description + "FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.") + (license license:gpl3+))) |