diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 132 |
1 files changed, 127 insertions, 5 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 0d3a765..75b9de7 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -374,11 +374,10 @@ association studies (GWAS).") (sha256 (base32 "09hvy9mf4dnmkb8qg49viffzrxk53m2kr4r955m84dxaa5pdrjhd")))) - (propagated-inputs `( + (propagated-inputs `( ;; propagated for development purposes ("python" ,python-2) ;; probably superfluous - ("r" ,r) - )) - (inputs `( + ("r" ,r) + ("redis" ,redis) ("mysql" ,mysql) ("gemma" ,gemma-git) ("pylmm-gn2" ,pylmm-gn2) @@ -405,7 +404,7 @@ association studies (GWAS).") ("python2-scipy" ,python2-scipy) ("python2-simplejson" ,python2-simplejson) ("python2-pyyaml" ,python2-pyyaml) - ("python-xlsxwriter" ,python-xlsxwriter) + ("python2-xlsxwriter" ,python2-xlsxwriter) ;; python-yolk is not needed ("plink" ,plink) ("qtlreaper" ,qtlreaper) @@ -419,3 +418,126 @@ association studies (GWAS).") (synopsis "Full genenetwork services") (description "Genenetwork installation sumo.") (license license:agpl3+)))) + +(define-public sambamba + (package + (name "sambamba") + (version "0.5.9") + (source (origin + (method url-fetch) + (uri (string-append + "https://github.com/lomereiter/sambamba/archive/v" + version ".tar.gz")) + (file-name (string-append "sambamba-" version ".tar.gz")) + (sha256 + (base32 "152zbg4m10ikr7xgk20c0nwqwrqvydmpc73p2c1fqmbhpk0l0ws6")))) + (build-system gnu-build-system) + (inputs + `(("ldc" ,ldc) + ;; These are currently included in "ldc". + ;;("druntime-ldc" ,druntime-ldc) + ;;("phobos2-ldc" ,phobos2-ldc) + ("lz4" ,lz4))) + (native-inputs + `(("ldc" ,ldc) + ;;("druntime-ldc" ,druntime-ldc) + ;;("phobos2-ldc" ,phobos2-ldc) + ("lz4" ,lz4) + ("gcc" ,gcc) + ("htslib-src" + ,(origin + (method url-fetch) + (uri (string-append + "https://github.com/lomereiter/htslib/archive/0.2.0-rc10.tar.gz")) + (file-name (string-append "htslib-0.2.0-rc10.tar.gz")) + (sha256 + (base32 "1k6dlf6m8yayhcp7b4yisgw1xqdy1xg2xyrllss6ld0wg00hfcbs")))) + ("biod-src" + ,(origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/biod/BioD.git") + (commit "7efdb8a2f7fdcd71c9ad9596be48d1262bb1bd5b"))) + (sha256 + (base32 "09icc2bjsg9y4hxjim4ql275izadf0kh1nnmapg8manyz6bc8svf")) + (file-name "biod"))))) + (arguments + '(#:phases + (modify-phases %standard-phases + (delete 'configure) + (add-after 'unpack 'unpack-htslib-sources + (lambda* (#:key inputs #:allow-other-keys) + ;; Unfortunately, the current build compiles htslib statically + ;; into the executable. Instead of patching the build files + ;; for Guix, this should be resolved on Sambamba upstream. For + ;; now, just extract the source code to the desired directory. + (and (with-directory-excursion "htslib" + (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src") + "--strip-components=1"))) + (zero? (system* "cp" "-R" (assoc-ref inputs "biod-src") "BioD"))))) + ;; Building a production-quality executable is done with a + ;; non-default make target. Adding it with #:make-flags breaks + ;; building tests. Therefore, the default make got replaced by this. + (replace + 'build + (lambda* (#:key (make-flags '()) #:allow-other-keys) + (zero? (system* "make" "sambamba-ldmd2-64" make-flags))))))) + (home-page "https://github.com/lomereiter/sambamba") + (synopsis "A tool for working with SAM and BAM files written in D.") + (description + "Sambamba is a high performance modern robust and fast tool (and +library), written in the D programming language, for working with SAM +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+))) |