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authorpjotrp2016-02-21 09:49:25 +0000
committerpjotrp2016-02-21 09:49:25 +0000
commit092c0c3a4a2b4a0b4f2b3cd6157fd6ad860316b9 (patch)
tree4528962182b678f88c2cd8c3cb1a011496ed9099
parent1574a0e0478e921905a2fad4ff3ff0f2c196b6f1 (diff)
parent5dbfda7d08ca718712a4c86bc3b7a6219843527a (diff)
downloadguix-bioinformatics-092c0c3a4a2b4a0b4f2b3cd6157fd6ad860316b9.tar.gz
conflict resolved
-rw-r--r--gn/packages/bioinformatics.scm90
1 files changed, 90 insertions, 0 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index af5cfba..1d65b4c 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -419,6 +419,45 @@ association studies (GWAS).")
(description "Genenetwork installation sumo.")
(license license:agpl3+))))
+(define-public rdmd
+ (package
+ (name "rdmd")
+ (version "20160217")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/D-Programming-Language/tools.git")
+ (commit "4dba6877c481c1a911a7d50714da8fbd80022f0e")))
+ (file-name (string-append name "-" version "-checkout"))
+ (sha256
+ (base32
+ "1pcx5lyqzrip86f4vv60x292rpvnwsq2hvl1znm9x9rn68f34m45"))))
+ (build-system gnu-build-system)
+ (arguments
+ '(#:phases
+ (modify-phases %standard-phases
+ (delete 'configure)
+ (delete 'check)
+ (replace
+ 'build
+ (lambda* _
+ (zero? (system* "ldc2" "rdmd.d"))))
+ (replace
+ 'install
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+ (mkdir-p bin)
+ (copy-file "rdmd" (string-append bin "/rdmd"))))))))
+ (native-inputs
+ `(("gcc" ,gcc)
+ ("ldc" ,ldc)))
+ (home-page "https://github.com/D-Programming-Language/tools/")
+ (synopsis "Extra tools for building D programs")
+ (description
+ "This repository hosts various tools redistributed with DMD or used
+internally during various build tasks.")
+ (license license:boost1.0)))
+
(define-public sambamba
(package
(name "sambamba")
@@ -444,6 +483,7 @@ association studies (GWAS).")
;;("phobos2-ldc" ,phobos2-ldc)
("lz4" ,lz4)
("gcc" ,gcc)
+ ("rdmd" ,rdmd)
("htslib-src"
,(origin
(method url-fetch)
@@ -492,3 +532,53 @@ 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 ""))))
+ (build-system gnu-build-system)
+ (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+)))