From 2c38581c2dcfa3c224f192bfff2c00d87afc8661 Mon Sep 17 00:00:00 2001 From: Muriithi Frederick Muriuki Date: Mon, 26 Mar 2018 17:47:21 +0300 Subject: gn: Update genenetwork3 definition * gn/packages/genenetwork.scm (genenetwork3): Update package definition. - Deactivate all packages that need Python 2 - Change the source uri for the package definition - Change the commit hash - Change the sha256 hash - Comment out the processing for pylmmcmd in the 'fix-paths' phase --- gn/packages/genenetwork.scm | 31 ++++++++++++++++++------------- 1 file changed, 18 insertions(+), 13 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 9aa723f..d605dd4 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -396,20 +396,24 @@ 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) @@ -436,6 +440,7 @@ location of a putative QTL.") ;; With Python3 support + ("python-wrapper" ,python-wrapper) ("gunicorn" ,gunicorn) ("python-rpy2" ,python-rpy2) ("python-flask" ,python-flask) @@ -458,12 +463,12 @@ 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 @@ -500,9 +505,9 @@ 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")) @@ -518,7 +523,7 @@ 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") -- cgit v1.2.3 From ea3f2e52986f5925df63e9fffa634aa267e25ec2 Mon Sep 17 00:00:00 2001 From: Muriithi Frederick Muriuki Date: Mon, 26 Mar 2018 18:10:26 +0300 Subject: Deactivate python 2 * With move to genenetwork3, we'll be using Python3, so forcing Python2 is no longer necessary. --- gn/packages/python.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index a6a99c6..a4b0955 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -210,7 +210,7 @@ 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 -- cgit v1.2.3 From ed82add468b0bc37eec68d17ec333257a23aa1bc Mon Sep 17 00:00:00 2001 From: Muriithi Frederick Muriuki Date: Wed, 4 Apr 2018 12:07:40 +0300 Subject: gn: Add new package * gn/packages/python.scm (python-htmlgen): New variable. --- gn/packages/python.scm | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) diff --git a/gn/packages/python.scm b/gn/packages/python.scm index a4b0955..ff8bf57 100644 --- a/gn/packages/python.scm +++ b/gn/packages/python.scm @@ -631,3 +631,24 @@ 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))) -- cgit v1.2.3 From fc284297def0b68c5a9fdd6c31cf9180b23fe73f Mon Sep 17 00:00:00 2001 From: Muriithi Frederick Muriuki Date: Wed, 4 Apr 2018 12:08:46 +0300 Subject: gn: Add package dependencies * gn/packages/genenetwork.scm (genenetwork3): - Add dependency python-cssselect - Add dependency python-htmlgen --- gn/packages/genenetwork.scm | 2 ++ 1 file changed, 2 insertions(+) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index d605dd4..9d8fd91 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -451,8 +451,10 @@ 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) -- cgit v1.2.3 From dbfa86d7ec182cdfcca003a991e4d87baf005791 Mon Sep 17 00:00:00 2001 From: Muriithi Frederick Muriuki Date: Mon, 11 Jun 2018 21:19:53 +0300 Subject: Remove Phewas * Phewas depends on an R package that no longer exists at the given url. This breaks the install. Phewas is also not currently used in genenetwork3. --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 8181e3e..56b5281 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -431,7 +431,7 @@ 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) -- cgit v1.2.3 From ed8342aae99e88b36459a85df7cc339a18b75591 Mon Sep 17 00:00:00 2001 From: Muriithi Frederick Muriuki Date: Thu, 21 Jun 2018 18:50:23 +0300 Subject: Add python-reaper * gn/packages/genenetwork.scm (python-reaper): New package. --- gn/packages/genenetwork.scm | 31 ++++++++++++++++++++++++++++++- 1 file changed, 30 insertions(+), 1 deletion(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 56b5281..bba25c0 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -399,6 +399,34 @@ location of a putative QTL.") (license license:agpl3+)))) + +(define-public python-reaper + (let (;;(commit "b8db1fb0857bc76a5881aba980a912fc774389ff") + (commit "a873abe18e3a7469c9c700aba6454fee69b32686")) + (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 + "140gzadz52dwfl2m1c8vwh6ckyl8q681w7rwfl1z1h8yw42nm2n7" + ;;"1mg4b6avf0fq8kjpxv3ag33ivsyrj0amhvna0kvyjj49aj1gmhr7" + ;; "0klgjra2qisfzs8mk0s8vzdr190l4n56xcm66dk0asqs7zswi8di" ;; default + )))) + (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") (commit "5bff4f49dffb4ac982d36cd0d39e0a9ec6bc66e9")) @@ -446,7 +474,6 @@ 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) @@ -454,11 +481,13 @@ 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) -- cgit v1.2.3 From 2f05ef36c428f92c9c46167b81fc6bf11b79505e Mon Sep 17 00:00:00 2001 From: Muriithi Frederick Muriuki Date: Thu, 28 Jun 2018 11:49:44 +0300 Subject: Update reaper commit --- gn/packages/genenetwork.scm | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index bba25c0..e7fab2c 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -401,8 +401,7 @@ location of a putative QTL.") (define-public python-reaper - (let (;;(commit "b8db1fb0857bc76a5881aba980a912fc774389ff") - (commit "a873abe18e3a7469c9c700aba6454fee69b32686")) + (let ((commit "63391333a6619771277bfffa9bd9d33811fa0d28")) (package (name "python-reaper") (version (string-append "0.0.1-" @@ -414,10 +413,7 @@ location of a putative QTL.") (commit commit))) (sha256 (base32 - "140gzadz52dwfl2m1c8vwh6ckyl8q681w7rwfl1z1h8yw42nm2n7" - ;;"1mg4b6avf0fq8kjpxv3ag33ivsyrj0amhvna0kvyjj49aj1gmhr7" - ;; "0klgjra2qisfzs8mk0s8vzdr190l4n56xcm66dk0asqs7zswi8di" ;; default - )))) + "1rq2qn0vrqd8k676yy8drm0zxzkj065ywhxjl0j1n2r25zifay7r")))) (build-system python-build-system) (arguments `(#:tests? #f)) -- cgit v1.2.3