diff options
Diffstat (limited to 'gn/packages')
| -rw-r--r-- | gn/packages/genenetwork.scm | 60 | ||||
| -rw-r--r-- | gn/packages/python.scm | 23 |
2 files changed, 68 insertions, 15 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 2998a3e..e7fab2c 100644 --- a/gn/packages/genenetwork.scm +++ b/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") diff --git a/gn/packages/python.scm b/gn/packages/python.scm index 23444f6..f254ce3 100644 --- a/gn/packages/python.scm +++ b/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))) |