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authorRoel Janssen2016-02-17 16:48:23 +0100
committerRoel Janssen2016-02-17 17:03:28 +0100
commitbe845af4f832d4b63ffb7fb50a9025553446864e (patch)
treeca50e4336ddf7d6085f184c99c30de11b43f77e2 /gn/packages
parentb3145ffd290341ec726c907ce329219caa3c99a7 (diff)
downloadguix-bioinformatics-be845af4f832d4b63ffb7fb50a9025553446864e.tar.gz
Added incomplete versions of FastQC and Picard.
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/bioinformatics.scm50
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+)))