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-rw-r--r--gn/packages/genenetwork.scm158
1 files changed, 158 insertions, 0 deletions
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