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Merge branch 'build/python3-migration'

master
Bonface Munyoki 1 year ago
parent
commit
9e188aba41
Signed by untrusted user: bonfacemunyoki GPG Key ID: F5BBAE1E0392253F
  1. 151
      gn/packages/genenetwork.scm

151
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
@ -347,7 +346,6 @@ 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)
@ -447,6 +445,155 @@ 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)
("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)
;; 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* ((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")
(("^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

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