From 4777f8a8615587d57c18c54c9d9d9ff7b3af0f2f Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Wed, 8 Jul 2020 01:51:00 +0300 Subject: gn: python3-genenetwork2: Add new package definition * gn/packages/genenetwork.scm (python3-genenetwork2): Add it. Same as genenetwork2 for now. --- gn/packages/genenetwork.scm | 158 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 158 insertions(+) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index e3e478b..27c583e 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -444,6 +444,164 @@ implemented, light on server resource usage, and fairly speedy.") (description "Genenetwork installation sumo.") (license license:agpl3+)))) +(define-public python3-genenetwork2 + (let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd") + (S specification->package)) + (package + (name "python3-genenetwork2") + (version (string-append "2.11-guix-" (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/genenetwork/genenetwork2_diet.git") + (commit commit))) + (file-name (string-append name "-" version)) + (sha256 + (base32 + "0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz")))) + (propagated-inputs + `(;; propagated for development purposes + ("python" ,python) ;; probably superfluous + ("coreutils" ,coreutils) + ("git" ,git) + ("vim" ,vim) + ("which" ,which) + ("grep" ,grep) + ("r" ,r) + ("r-ctl" ,r-ctl) + ; ("r-phewas" ,r-phewas) + ("r-qtl" ,r-qtl) + ("r-wgcna" ,r-wgcna) + ("redis" ,redis) + ("mariadb" ,mariadb) + ("gemma" ,gemma-gn2) + ("gemma-wrapper" ,gemma-wrapper) + ("plink-ng-gn" ,plink-ng-gn) + ("rust-qtlreaper" ,rust-qtlreaper) + ("nginx" ,nginx) + ("python-twint" ,python-twint) + ("python-flask" ,python-flask) + ("gunicorn" ,gunicorn) + ("python-pillow" ,python-pillow) + ;; ("python2-pil1" ,python2-pil1-gn) + ("python2-piddle-gn" ,python2-piddle-gn) ; DEPRECATED + ("python-cssselect" ,python-cssselect) + ("python-elasticsearch" ,python-elasticsearch) + ("python-htmlgen" ,python-htmlgen) + ("python-jinja2" ,python-jinja2) + ("python-sqlalchemy" ,python-sqlalchemy) + ("python-flask-sqlalchemy" ,python-flask-sqlalchemy) + ("python-setuptools" ,python-setuptools) + ("python-scipy" ,python-scipy) + ("python-lxml" ,python-lxml) + ("python-mechanize" ,python-mechanize) + ("python-mysqlclient" ,python-mysqlclient) + ("python2-numarray" ,python2-numarray) ; DEPRECATED + ("python-numpy" ,python-numpy) + ("python-pandas" ,python-pandas) + ("python2-parallel" ,python2-parallel) ; TODO + ("python-parameterized" ,python-parameterized) + ("python-passlib" ,python-passlib) + ("python-redis" ,python-redis) + ("python-requests" ,python-requests) + ("python2-rpy2" ,python2-rpy2) ; TODO + ("python-simplejson" ,python-simplejson) + ("python-pyyaml" ,python-pyyaml) + ("python-unittest2" ,python-unittest2) + ("python-xlsxwriter" ,python-xlsxwriter) + ("python2-qtlreaper" ,python2-qtlreaper) ; Deprecated + ;; All the external js dependencies + ("javascript-cytoscape" ,javascript-cytoscape) + ("javascript-panzoom" ,javascript-cytoscape-panzoom) + ("javascript-qtip" ,javascript-cytoscape-qtip) + ("javascript-chroma" ,javascript-chroma) + ("javascript-d3-tip" ,javascript-d3-tip) + ("javascript-jscolor" ,javascript-jscolor) + ("javascript-colorbox" ,javascript-colorbox) + ("javascript-jszip" ,javascript-jszip) + ("js-jstat" ,js-jstat) + ("js-md5" ,js-md5) + ("js-parsley" ,js-parsley) + ("javascript-plotly" ,javascript-plotly) + ("javascript-typeahead" ,javascript-typeahead) + ("js-underscore" ,js-underscore) + ("js-smart-time-ago" ,js-smart-time-ago) + ("javascript-nouislider" ,javascript-nouislider) + ("javascript-purescript-genome-browser" ,javascript-purescript-genome-browser) + ("javascript-datatables" ,javascript-datatables) + ("javascript-datatables-scroller" ,javascript-datatables-scroller) + ("javascript-datatables-buttons" ,javascript-datatables-buttons) + ("javascript-datatables-buttons-bootstrap" ,javascript-datatables-buttons-bootstrap) + ("javascript-datatables-plugins" ,javascript-datatables-plugins) + ("javascript-datatables-col-reorder" ,javascript-datatables-col-reorder) + ("javascript-datatables-col-resize" ,javascript-datatables-col-resize) + ("javascript-datatables-buttons-styles" ,javascript-datatables-buttons-styles) + ("javascript-shapiro-wilk" ,javascript-shapiro-wilk) + ("javascript-underscore-string" ,javascript-underscore-string) + ("javascript-qtip2" ,javascript-qtip2) + ("javascript-d3js" ,javascript-d3js) + ("javascript-nvd3" ,javascript-nvd3) + ("javascript-bootstrap" ,javascript-bootstrap) + ("javascript-jquery" ,javascript-jquery) + ("javascript-zxcvbn-async" ,javascript-zxcvbn-async) + ("javascript-jquery-ui" ,javascript-jquery-ui) + ("javascript-jquery-cookie" ,javascript-jquery-cookie) + )) + (inputs + `(("javascript-colorbox" ,(package-source javascript-colorbox)))) + (build-system python-build-system) + (arguments + `(#:python ,python-2 + #:phases + (modify-phases %standard-phases + (delete 'reset-gzip-timestamps) + (add-after 'unpack 'fix-paths-scripts + (lambda _ + (substitute* "bin/genenetwork2" + (("/usr/bin/env") (which "env")) + (("python ") (string-append (which "python2") " ")) + (("readlink") (which "readlink")) + (("dirname") (which "dirname")) + (("basename") (which "basename")) + (("cat") (which "cat")) + (("echo") (which "echo")) + (("redis-server") (which "redis-server")) + (("git") (which "git")) + (("grep") (which "grep")) + (("rm") (which "rm")) + (("which") (which "which")) ; three whiches in a row! + ) + #t)) + (add-after 'unpack 'patch-javascript + (lambda* (#:key inputs #:allow-other-keys) + (let ((colorbox (assoc-ref inputs "javascript-colorbox")) + (gn2 "/share/genenetwork2/javascript/")) + (delete-file-recursively "wqflask/wqflask/static/packages/colorbox") + (copy-recursively colorbox "wqflask/wqflask/static/packages/colorbox") + #t))) + (add-before 'install 'fix-paths + (lambda* (#:key inputs #:allow-other-keys) + (let* ( + ; (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2")) + ; (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) + (plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) + (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) + ) + + (substitute* '("etc/default_settings.py") + ; (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) + ; (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) + (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) + (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) + ) + )))) + #:tests? #f)) ; no 'setup.py test' + (home-page "http://genenetwork.org/") + (synopsis "Full genenetwork services") + (description "Genenetwork installation sumo.") + (license license:agpl3+)))) + ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x -- cgit v1.2.3 From 8e2547aeba66e76b81022c0d0275bef48806afc4 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 10 Jul 2020 02:26:35 +0300 Subject: gn: python3-genenetwork2: Remove python-qtlreaper * gn/packages/genenetwork.scm (python3-genenetwork2): Remove deprecated python2-qtlreaper --- gn/packages/genenetwork.scm | 1 - 1 file changed, 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 27c583e..6fbb6c3 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -510,7 +510,6 @@ implemented, light on server resource usage, and fairly speedy.") ("python-pyyaml" ,python-pyyaml) ("python-unittest2" ,python-unittest2) ("python-xlsxwriter" ,python-xlsxwriter) - ("python2-qtlreaper" ,python2-qtlreaper) ; Deprecated ;; All the external js dependencies ("javascript-cytoscape" ,javascript-cytoscape) ("javascript-panzoom" ,javascript-cytoscape-panzoom) -- cgit v1.2.3 From 5fd9f2e2fd64c98cbdb20add5e5111c428746841 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 10 Jul 2020 02:28:38 +0300 Subject: gn: python3-genenetwork2: Remove python2-parallel * gn/packages/genenetwork.scm (python3-genenetwork): Remove deprecated package --- gn/packages/genenetwork.scm | 1 - 1 file changed, 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 6fbb6c3..4c2854f 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -500,7 +500,6 @@ implemented, light on server resource usage, and fairly speedy.") ("python2-numarray" ,python2-numarray) ; DEPRECATED ("python-numpy" ,python-numpy) ("python-pandas" ,python-pandas) - ("python2-parallel" ,python2-parallel) ; TODO ("python-parameterized" ,python-parameterized) ("python-passlib" ,python-passlib) ("python-redis" ,python-redis) -- cgit v1.2.3 From 7a238bf65f04afecee0663ced5d972e55720391c Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Fri, 10 Jul 2020 15:39:43 +0300 Subject: gn: python3-genenetwork2: Remove unnecessary comments --- gn/packages/genenetwork.scm | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4c2854f..4711fbc 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -290,7 +290,6 @@ implemented, light on server resource usage, and fairly speedy.") (method git-fetch) (uri (git-reference (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 @@ -580,16 +579,9 @@ implemented, light on server resource usage, and fairly speedy.") #t))) (add-before 'install 'fix-paths (lambda* (#:key inputs #:allow-other-keys) - (let* ( - ; (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2")) - ; (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis")) - (plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) - (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma")) - ) - + (let* ((plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2")) + (gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))) (substitute* '("etc/default_settings.py") - ; (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )) - ; (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" )) (("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" )) (("^GEMMA_COMMAND =.*") (string-append "GEMMA_COMMAND = \"" gemmacmd "\"\n" )) ) -- cgit v1.2.3 From fbd7fa2b583fce2a43f4f47747f0dbdab8878909 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 23 Jul 2020 13:45:32 +0300 Subject: gn: python3-genenetwork2: Remove duplicate requests input * gn/packages/genenetwork.scm (python3-genenetwork2): Delete duplicate input --- gn/packages/genenetwork.scm | 1 - 1 file changed, 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index 4711fbc..cc981e0 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -343,7 +343,6 @@ implemented, light on server resource usage, and fairly speedy.") ("python2-passlib" ,python2-passlib) ("python2-redis" ,python2-redis) ("python2-requests" ,python2-requests) - ("python2-requests" ,python2-requests) ("python2-rpy2" ,python2-rpy2) ("python2-scipy" ,python2-scipy) ("python2-simplejson" ,python2-simplejson) -- cgit v1.2.3 From 4e318da7467d0439b55864b88cd9d95c17e37b24 Mon Sep 17 00:00:00 2001 From: BonfaceKilz Date: Thu, 23 Jul 2020 13:47:24 +0300 Subject: gn: python3-genenetwork: Rename unittest2 input --- gn/packages/genenetwork.scm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'gn/packages/genenetwork.scm') diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm index cc981e0..671d5e9 100644 --- a/gn/packages/genenetwork.scm +++ b/gn/packages/genenetwork.scm @@ -347,7 +347,7 @@ implemented, light on server resource usage, and fairly speedy.") ("python2-scipy" ,python2-scipy) ("python2-simplejson" ,python2-simplejson) ("python2-pyyaml" ,python2-pyyaml) - ("python2-unittest2" ,python2-unittest2) + ("python-unittest2" ,python-unittest2) ("python2-xlsxwriter" ,python2-xlsxwriter) ("python2-qtlreaper" ,python2-qtlreaper) ;; All the external js dependencies -- cgit v1.2.3