diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 68 |
1 files changed, 1 insertions, 67 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 0798822..3a82c18 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -77,7 +77,7 @@ (propagated-inputs `(("python" ,python-2) ("r" ,r) - ("r-dnacopy" ,r-dnacopy) + ;; ("r-dnacopy" ,r-dnacopy) <-- missing in Pjotr's tree ("bedtools" ,bedtools) ("samtools" ,samtools))) (arguments @@ -1048,72 +1048,6 @@ subset of samtools functionality, including view, index, sort, markdup, and depth.") (license license:gpl2+)))) -(define-public genenetwork2 - (let ((commit "234aa9820eeaa3e4611239de31de1ba526d8bf09")) - (package - (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"))) - (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+))) (define-public vcflib (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb")) |