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-rw-r--r--gn/packages/genenetwork.scm33
-rw-r--r--gn/packages/python.scm23
2 files changed, 42 insertions, 14 deletions
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index 2998a3e..8181e3e 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -400,20 +400,24 @@ location of a putative QTL.")
(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)
@@ -442,6 +446,7 @@ location of a putative QTL.")
("javascript-qtip" ,javascript-cytoscape-qtip)
;; With Python3 support
+ ("python-wrapper" ,python-wrapper)
("gunicorn" ,gunicorn)
("python-rpy2" ,python-rpy2)
("python-flask" ,python-flask)
@@ -452,8 +457,10 @@ location of a putative QTL.")
("python-pyyaml" ,python-pyyaml)
("python-jinja2" ,python-jinja2)
("python-pandas" ,python-pandas)
+ ("python-htmlgen" ,python-htmlgen)
("python-passlib" ,python-passlib)
("python-requests" ,python-requests)
+ ("python-cssselect" ,python-cssselect)
("python-sqlalchemy" ,python-sqlalchemy)
("python-setuptools" ,python-setuptools)
("python-simplejson" ,python-simplejson)
@@ -464,12 +471,12 @@ 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 +513,9 @@ 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 +531,7 @@ 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)))