diff options
| -rw-r--r-- | gn/packages/bioinformatics.scm | 88 |
1 files changed, 52 insertions, 36 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index a4d14b0..0798822 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1048,43 +1048,59 @@ subset of samtools functionality, including view, index, sort, markdup, and depth.") (license license:gpl2+)))) -(define-public picard +(define-public genenetwork2 + (let ((commit "234aa9820eeaa3e4611239de31de1ba526d8bf09")) (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) + (name "genenetwork2") + (version (string-append "2.0-" (string-take commit 7) )) + (source (origin + (method git-fetch) + (uri (git-reference + ;; (url "https://github.com/genenetwork/genenetwork2.git") + ;; (url "https://github.com/pjotrp/genenetwork2.git") + (url "https://github.com/genenetwork/genenetwork2_diet.git") + (commit commit))) + (file-name (string-append name "-" (string-take commit 7))) + (sha256 + (base32 + "10knws2azy53bar615r0b1dk6nr9lrl0x25k7vsc6jm879wcp91b")))) + (propagated-inputs `( + ("python" ,python-2) ;; probably superfluous + ("r" ,r) + )) + (inputs `( + ("mysql" ,mysql) + ("gemma" ,gemma-git) + ("plink2" ,plink-ng) + ("nginx" ,nginx) + ("python2-flask" ,python2-flask) + ("python2-htmlgen-gn" ,python2-htmlgen-gn) + ("python2-jinja2" ,python2-jinja2) + ("python2-sqlalchemy" ,python2-sqlalchemy) + ("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy) + ("python2-setuptools" ,python2-setuptools) + ("python2-scipy" ,python2-scipy) + ;; looks like python-numarray is not needed + ("python2-mysqlclient" ,python2-mysqlclient) + ("python2-numarray" ,python2-numarray) + ("python2-numpy" ,python2-numpy) + ("python2-pandas" ,python2-pandas) + ("python2-parallel" ,python2-parallel) + ("python2-passlib" ,python2-passlib) + ("python2-piddle" ,python2-piddle) + ("python2-redis" ,python2-redis) + ("python2-requests" ,python2-requests) + ("python2-rpy2" ,python2-rpy2) + ("python2-scipy" ,python2-scipy) + ("python2-simplejson" ,python2-simplejson) + ("python2-pyyaml" ,python2-pyyaml) + ("python2-xlsxwriter" ,python-xlsxwriter) + ;; python-yolk is not needed + ("plink" ,plink) + ("qtlreaper" ,qtlreaper) + ("r-qtl" ,r-qtl) + )) + (build-system python-build-system) (arguments `(("perl" ,perl) ; Needed to run the java command. ("jdk" ,icedtea "jdk"))) |