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Merge branch 'master' of gitlab.com:fredmanglis/guix-bioinformatics

* Merge changes to genenetwork3 package.
gn-stable
Muriithi Frederick Muriuki 4 years ago
parent
commit
0b02fa474b
  1. 60
      gn/packages/genenetwork.scm
  2. 23
      gn/packages/python.scm

60
gn/packages/genenetwork.scm

@ -399,21 +399,49 @@ location of a putative QTL.")
(license license:agpl3+))))
(define-public python-reaper
(let ((commit "63391333a6619771277bfffa9bd9d33811fa0d28"))
(package
(name "python-reaper")
(version (string-append "0.0.1-"
(string-take commit 7)))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/fredmanglis/reaper.git")
(commit commit)))
(sha256
(base32
"1rq2qn0vrqd8k676yy8drm0zxzkj065ywhxjl0j1n2r25zifay7r"))))
(build-system python-build-system)
(arguments
`(#:tests? #f))
(home-page "https://github.com/fredmanglis/reaper")
(synopsis "Parser for .geno files")
(description "Parser for .geno files. It replaces the Python2 library
written in C")
(license license:agpl3+))))
(define-public genenetwork3
(let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd"))
(let (;; (commit "1538ffd33af19e6ac922b4ee85fe701408968dfd")
(commit "5bff4f49dffb4ac982d36cd0d39e0a9ec6bc66e9"))
(package
(name "genenetwork3")
(version (string-append "2.10rc5-" (string-take commit 7) ))
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git")
(url "https://github.com/fredmanglis/genenetwork2.git")
;; (url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git")
;; (url "https://github.com/genenetwork/genenetwork2_diet.git")
(commit commit)))
(file-name (string-append name "-" version))
(sha256
(base32
"0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz"))))
"0klgjra2qisfzs8mk0s8vzdr190l4n56xcm66dk0asqs7zswi8di"
;; "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz"
))))
(propagated-inputs ;; propagated for development purposes
`( ;; Agnostic to Python
("r" ,r)
@ -427,7 +455,7 @@ location of a putative QTL.")
("mysql" ,mysql)
("nginx" ,nginx)
("r-wgcna" ,r-wgcna)
("r-phewas" ,r-phewas)
;; ("r-phewas" ,r-phewas)
("coreutils" ,coreutils)
("gemma" ,gemma-gn2-git)
("plink-ng-gn" ,plink-ng-gn)
@ -449,11 +477,15 @@ location of a putative QTL.")
("python-numpy" ,python-numpy)
("python-redis" ,python-redis)
("python-scipy" ,python-scipy)
("python-reaper" ,python-reaper)
("python-pyyaml" ,python-pyyaml)
("python-jinja2" ,python-jinja2)
("python-pandas" ,python-pandas)
("python-htmlgen" ,python-htmlgen)
("python-passlib" ,python-passlib)
("python-wrapper" ,python-wrapper)
("python-requests" ,python-requests)
("python-cssselect" ,python-cssselect)
("python-sqlalchemy" ,python-sqlalchemy)
("python-setuptools" ,python-setuptools)
("python-simplejson" ,python-simplejson)
@ -464,12 +496,12 @@ location of a putative QTL.")
;; Without Python3 support
("python-qtlreaper" ,python-qtlreaper) ;; Run as an external program
("pylmm-gn2" ,pylmm-gn2) ;; To be run as an external python2 program
("python2-pil1" ,python2-pil1) ; should move to pillow some day. Run as external python2 program
("python2-numarray" ,python2-numarray) ;; Update gn2 code and drop this (IMPORTANT)
("python2-piddle-gn" ,python2-piddle-gn) ;; Run as external python2 program
("python2-htmlgen-gn" ,python2-htmlgen-gn) ;; pjotrp and zsloan to give directions
;; ("python-qtlreaper" ,python-qtlreaper) ;; Run as an external program
;; ("pylmm-gn2" ,pylmm-gn2) ;; To be run as an external python2 program
;; ("python2-pil1" ,python2-pil1) ; should move to pillow some day. Run as external python2 program
;; ("python2-numarray" ,python2-numarray) ;; Update gn2 code and drop this (IMPORTANT)
;; ("python2-piddle-gn" ,python2-piddle-gn) ;; Run as external python2 program
;; ("python2-htmlgen-gn" ,python2-htmlgen-gn) ;; pjotrp and zsloan to give directions
;; Removed packages
@ -506,9 +538,9 @@ location of a putative QTL.")
(string-append
(assoc-ref inputs "genenetwork2-files-small")
"/share/genenetwork2" ))
(pylmmcmd
(string-append
(assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis"))
;; (pylmmcmd
;; (string-append
;; (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis"))
(plink2cmd
(string-append
(assoc-ref inputs "plink-ng-gn") "/bin/plink2"))
@ -524,7 +556,7 @@ location of a putative QTL.")
(("^PLINK_COMMAND =.*")
(string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
(("^GEMMA_COMMAND =.*")
(string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )))))))
(string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n")))))))
#:tests? #f)) ; no 'setup.py test'
(home-page "http://genenetwork.org/")
(synopsis "Full genenetwork services")

23
gn/packages/python.scm

@ -176,7 +176,7 @@ functions.")
(propagated-inputs
`(("inotify-tools" ,inotify-tools)))
(arguments `(
#:python ,python-2 ; GN2 is still python2
;; #:python ,python-2 ; GN2 is still python2
#:tests? #f)) ;; No tests.
(home-page "http://gunicorn.org")
(synopsis
@ -597,3 +597,24 @@ objects using the same basic infrastructure and syntax. Numarray is
now part of the numpy package, though some legacy software still uses
the older versions.")
(license license:gpl2))) ; actualy PyRAF http://www.stsci.edu/resources/software_hardware/pyraf/LICENSE
(define-public python-htmlgen
(package
(name "python-htmlgen")
(version "1.0.0")
(source
(origin
(method url-fetch)
(uri (string-append
"https://github.com/srittau/python-htmlgen/archive/v"
version ".tar.gz"))
(sha256
(base32
"1rwgqxhmc93l60wf4ay7ph619710kvyp73s22i0snjpm5i0bhc46"))))
(build-system python-build-system)
(arguments
`(#:tests? #f))
(synopsis "Python HTML 5 Generator")
(description "This is a python library for generating html from classes.")
(home-page "https://github.com/srittau/python-htmlgen")
(license license:expat)))
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