diff options
Diffstat (limited to 'gn')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 90 |
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+))) |