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authorpjotrp2017-05-18 10:26:16 +0000
committerpjotrp2017-05-18 10:26:16 +0000
commit0d46a521faaaa121687bb634ba0388de83825048 (patch)
treee0eaf9b24897b9f708411cdf27d68246ccdfad34 /gn
parent774fcf1e81b820e4bb5e0ddd5db2edb37bb9ff4b (diff)
downloadguix-bioinformatics-0d46a521faaaa121687bb634ba0388de83825048.tar.gz
Remove gn1 and update gn2
Diffstat (limited to 'gn')
-rw-r--r--gn/packages/genenetwork.scm56
1 files changed, 2 insertions, 54 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 0e0d02e..70cb928 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -123,60 +123,8 @@ bootstrap resampling to estimate the confidence region for the
location of a putative QTL.")
(license license:gpl2+))))
-(define-public genenetwork1 ; guix incomplete
- (let ((commit "d622c803b"))
- (package
- (name "genenetwork1")
- (version (string-append "1.0-" commit ))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/genenetwork/genenetwork.git")
- ;; (url "https://github.com/pjotrp/genenetwork.git")
- (commit commit)))
- (file-name (string-append name "-" commit))
- (sha256
- (base32
- "14fzfcm4vl20mlhxjslfa01i1nmxpk8lbxmfvpq6dyfc22ir62py"))))
- (propagated-inputs `(
- ("python" ,python-2) ;; probably superfluous
- ("r" ,r)
- ))
- (inputs `(
- ;; http://spring211.uthsc.edu/gn/thirdparty.tbz
- ;; graphviz-2.22.2 htmlgen json numarray-1.5.2 piddle PIL pp-1.5.7 pyx pyXLWriter svg
- ("mysql" ,mysql)
- ("nginx" ,nginx)
- ("graphviz" ,graphviz)
- ; ("python2-jinja2" ,python2-jinja2)
- ; ("python2-sqlalchemy" ,python2-sqlalchemy)
- ; ("python2-setuptools" ,python2-setuptools)
- ; ("python2-scipy" ,python2-scipy)
- ;; looks like python-numarray is not needed
- ; ("python2-numpy" ,python2-numpy)
- ; ("python2-pandas" ,python2-pandas)
- ; ("python2-passlib" ,python2-passlib)
- ; ("python2-redis" ,python2-redis)
- ; ("python2-requests" ,python2-requests)
- ; ("python2-simplejson" ,python2-simplejson)
- ; ("python2-pyyaml" ,python2-pyyaml)
- ;; python-yolk is not needed
- ("python2-pil" ,python2-pil)
- ("python2-numarray" ,python2-numarray)
- ("plink" ,plink) ;; gn1
- ; ("r-qtl" ,r-qtl)
- ))
- (build-system python-build-system)
- (arguments
- `(#:python ,python-2
- #:tests? #f)) ; no 'setup.py test'
- (home-page "http://genenetwork.org/")
- (synopsis "Full genenetwork services")
- (description "Genenetwork installation sumo.")
- (license license:agpl3+))))
-
(define-public genenetwork2
- (let ((commit "48c04bb5c6a8d974697f6904857ebd377c4c0ce5"))
+ (let ((commit "5fa50d0779ea8a8713b0fba9ee45ecd50e6f28e3"))
(package
(name "genenetwork2")
(version (string-append "2.10rc2-" (string-take commit 7) ))
@@ -189,7 +137,7 @@ location of a putative QTL.")
(file-name (string-append name "-" (string-take commit 7)))
(sha256
(base32
- "0mwhq3w436xk57p02kjwmjl2xjbi3m1s0a6m2qk54bpr1k50zxqi"))))
+ "1z674057hcmfv58b0k2v4n1wgcrnfpshpr3xhm2nchwm22lq8krw"))))
(propagated-inputs `( ;; propagated for development purposes
("python" ,python-2) ;; probably superfluous
("r" ,r)