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-rw-r--r--gn/packages/bioinformatics.scm88
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")))