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7 Commits

  1. 2
      README.org
  2. 51
      gn/packages/genenetwork.scm
  3. 14
      gn/packages/statistics.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]]:

51
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 +190,52 @@ 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)))))
(propagated-inputs
`(("python-eventlet" ,python-eventlet) ; we may drop this in favour of gevent
("python-gevent" ,python-gevent)))
(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 +319,7 @@ 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 +355,7 @@ 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))))

14
gn/packages/statistics.scm

@ -328,20 +328,18 @@ for use in genome-wide association studies (GWAS).")
(sha256
(base32
"027cij4vdsq3xhi38izzn07q6xwja7n8v95l7kk1pp92y9qkvqv3"))))
(build-system r-build-system)
(inputs `(
("r-qtl" ,r-qtl)
("r-mass" ,r-mass)
(build-system r-build-system) (inputs `(
("r-qtl" ,r-qtl) ("r-mass" ,r-mass)
))
(home-page "https://github.com/DannyArends/CTLmapping")
(synopsis "R package for analysis of genetical genomic data to identify genetic loci associated with correlation changes in quantitative traits (CTL)")
(synopsis "R package for analysis of genetical genomic data to identify genetic loci associated with corr
elation changes in quantitative traits (CTL)")
(description "Analysis of experimental crosses to identify genetic
markers associated with correlation changes in quantitative
traits (CTL). The additional correlation information obtained can be
combined with QTL information to perform de novo reconstruction of
traits (CTL). The additional correlation information obtained can be combined with QTL information to perform de novo reconstruction of
interaction networks.")
(license license:gpl3)))
(define-public gsl1 ; supporting older GSL tests - no longer really used
(package

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