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authorpjotrp2016-03-23 18:28:27 -0500
committerpjotrp2016-03-23 18:28:27 -0500
commitd81eb54552568897e9a3c9cd52b352b2c0644565 (patch)
tree9a0159e9e0255a227ee122bd69146d62b12c5ce1 /gn/packages
parent5b3413b0b490a72df1dd1ca108559698948b955f (diff)
downloadguix-bioinformatics-d81eb54552568897e9a3c9cd52b352b2c0644565.tar.gz
This runs with gn-stable
Diffstat (limited to 'gn/packages')
-rw-r--r--gn/packages/bioinformatics.scm68
-rw-r--r--gn/packages/genenetwork.scm2
2 files changed, 2 insertions, 68 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"))
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 79ad3fe..1382cfb 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -223,7 +223,7 @@
;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip
;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x
-(define-public genenetwork2-files-small1
+(define-public genenetwork2-files-small
(let ((pfff "xx"))
(package
(name "genenetwork2-files-small")