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4 Commits

  1. 2
      README.org
  2. 48
      gn/packages/genenetwork.scm

2
README.org

@ -9,6 +9,8 @@ interest can be found at
2. https://github.com/UMCUGenetics/guix-additions
3. https://github.com/ekg/guix-genomics
Also see [[http://git.genenetwork.org/pjotrp/guix-notes/src/branch/master/CHANNELS.org][Guix notes]] for a list of channels.
To easily use the packages from this repo, simply add it to your
`channels` list in ~/.config/guix/channels.scm as described
[[https://guix.gnu.org/manual/en/html_node/Channels.html][here]]:

48
gn/packages/genenetwork.scm

@ -42,6 +42,8 @@
#:use-module (gn packages python24)
#:use-module (gn packages statistics))
(define-public my-deploy
(package
(name "my-deploy")
@ -188,6 +190,49 @@ bootstrap resampling to estimate the confidence region for the
location of a putative QTL.")
(license license:gpl2+))))
;; Reintroduced python2-gunicorn because we are running GN with python2
;; right now. Please keep it until we migrate to Python3 fully!
(define-public python-gunicorn-gn
(package
(name "python-gunicorn-gn")
(version "19.9.0")
(source
(origin
(method url-fetch)
(uri (pypi-uri "gunicorn" version))
(sha256
(base32
"1wzlf4xmn6qjirh5w81l6i6kqjnab1n1qqkh7zsj1yb6gh4n49ps"))))
(build-system python-build-system)
(inputs
`(("python-mock" ,python-mock)))
(arguments
'(#:phases
(modify-phases %standard-phases
(add-after 'unpack 'loosen-verion-restrictions
(lambda _
(substitute* "requirements_test.txt"
(("coverage.*") "coverage\n")
(("pytest.*") "pytest\n")
(("pytest-cov.*") "pytest-cov\n"))
#t)))))
(native-inputs
`(("python-coverage" ,python-coverage)
("python-pytest" ,python-pytest)
("python-pytest-cov" ,python-pytest-cov)))
(home-page "https://gunicorn.org")
(synopsis "WSGI HTTP Server for UNIX")
(description "Gunicorn 'Green Unicorn' is a Python WSGI HTTP Server for
UNIX. It's a pre-fork worker model ported from Ruby's Unicorn project. The
Gunicorn server is broadly compatible with various web frameworks, simply
implemented, light on server resource usage, and fairly speedy.")
(license license:expat)))
(define-public python2-gunicorn-gn
(package-with-python2 python-gunicorn-gn))
(define-public rust-qtlreaper
(let ((commit "2e7fed6d45b0b602d80fa2a55835f96ef1cba9e3")
@ -271,7 +316,7 @@ location of a putative QTL.")
("rust-qtlreaper" ,rust-qtlreaper)
("nginx" ,nginx)
("python2-flask" ,python2-flask)
("gunicorn" ,gunicorn)
("python2-gunicorn-gn" ,python2-gunicorn-gn)
; ("python2-pillow" ,python2-pillow) - for later!
("python2-pil1" ,python2-pil1-gn)
("python2-piddle-gn" ,python2-piddle-gn)
@ -307,6 +352,7 @@ location of a putative QTL.")
("javascript-cytoscape" ,javascript-cytoscape)
("javascript-panzoom" ,javascript-cytoscape-panzoom)
("javascript-qtip" ,javascript-cytoscape-qtip)
("javascript-datatables" ,javascript-datatables)
))
(inputs
`(("javascript-colorbox" ,(package-source javascript-colorbox))))

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