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889 lines
39 KiB
889 lines
39 KiB
;; Bioinformatics module
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(define-module (gn packages genenetwork)
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#:use-module ((guix licenses) #:prefix license:)
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#:use-module (guix packages)
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#:use-module (guix utils)
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#:use-module (guix download)
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#:use-module (guix git-download)
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#:use-module (guix build-system cargo)
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#:use-module (guix build-system gnu)
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#:use-module (guix build-system python)
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#:use-module (guix build-system trivial)
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#:use-module (guix graph)
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#:use-module (guix scripts graph)
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#:use-module (guix store)
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#:use-module (gnu packages)
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#:use-module (gnu packages base)
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#:use-module (gnu packages bioconductor)
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#:use-module (gnu packages bioinformatics)
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#:use-module (gnu packages bootstrap)
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#:use-module (gnu packages check)
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#:use-module (gnu packages cran)
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#:use-module (gnu packages crates-io)
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#:use-module (gnu packages compression)
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#:use-module (gnu packages databases)
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#:use-module (gnu packages ghostscript)
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#:use-module (gnu packages graphviz)
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#:use-module (gnu packages parallel)
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#:use-module (gnu packages python)
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#:use-module (gnu packages python-check)
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#:use-module (gnu packages python-crypto)
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#:use-module (gnu packages python-science)
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#:use-module (gnu packages python-web)
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#:use-module (gnu packages python-xyz)
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#:use-module (gnu packages rdf)
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#:use-module (gnu packages rust)
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#:use-module (gnu packages scheme)
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#:use-module (gnu packages statistics)
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#:use-module (gnu packages version-control)
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#:use-module (gnu packages vim)
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#:use-module (gnu packages web)
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#:use-module (gnu packages wget)
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#:use-module (gnu packages xml)
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#:use-module (past packages python)
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#:use-module (past packages web)
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#:use-module (gn packages bioinformatics)
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#:use-module (gn packages twint)
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#:use-module (gn packages databases)
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#:use-module (gn packages elixir)
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#:use-module (gn packages gemma)
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#:use-module (gn packages javascript)
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#:use-module (gn packages phewas)
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#:use-module (gn packages python)
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#:use-module (gn packages python24)
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#:use-module (gn packages statistics)
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#:use-module (gn packages web)
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#:use-module (srfi srfi-1))
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(define-public python2-qtlreaper
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(let ((commit "442c217b90393380a8634ff8636b44992f5c53dd"))
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(package
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(name "python2-qtlreaper")
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(version (string-append "1.11-gn2-" (string-take commit 7) ))
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(source (origin
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(method git-fetch)
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(uri (git-reference
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;; (url "https://github.com/genenetwork/genenetwork2.git")
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(url "https://github.com/pjotrp/QTLreaper.git")
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(commit commit)))
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(file-name (string-append name "-" (string-take commit 7)))
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(sha256
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(base32
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"1rrbm1ap2zzyjxmrs9aa1d18sgiba5dhj1fmkl7wmab06jv3j1hm"))))
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(build-system python-build-system)
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(arguments
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`(#:python ,python-2
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#:tests? #f)) ; no 'setup.py test' really!
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(home-page "http://qtlreaper.sourceforge.net/")
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(synopsis "Scan expression data for QTLs")
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(description
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"Batch-oriented version of WebQTL. It requires, as input,
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expression data from members of a set of recombinant inbred lines and
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genotype information for the same lines. It searches for an
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association between each expression trait and all genotypes and
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evaluates that association by a permutation test. For the permutation
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test, it performs only as many permutations as are necessary to define
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the empirical P-value to a reasonable precision. It also performs
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bootstrap resampling to estimate the confidence region for the
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location of a putative QTL.")
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(license license:gpl2+))))
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(define-public python24-qtlreaper
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(let ((commit "442c217b90393380a8634ff8636b44992f5c53dd"))
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(package
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(name "python24-qtlreaper")
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(version (git-version "1.11" "gn1" commit))
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(source (origin
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(method git-fetch)
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(uri (git-reference
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;; (url "https://github.com/genenetwork/genenetwork2.git")
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(url "https://github.com/pjotrp/QTLreaper.git")
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(commit commit)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"1rrbm1ap2zzyjxmrs9aa1d18sgiba5dhj1fmkl7wmab06jv3j1hm"))))
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(build-system python-build-system)
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(arguments
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`(#:python ,python-2.4
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#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'make-max-markername-size-larger
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(lambda _
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(substitute* "Src/dataset.c"
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(("512") "2048"))
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#t))
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(replace 'check
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(lambda* (#:key inputs outputs #:allow-other-keys)
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(add-installed-pythonpath inputs outputs)
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(invoke "python" "test/runtest.py"))))))
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(native-inputs
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`(("python24-setuptools" ,python24-setuptools)))
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(home-page "http://qtlreaper.sourceforge.net/")
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(synopsis "Scan expression data for QTLs")
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(description
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"Batch-oriented version of WebQTL. It requires, as input,
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expression data from members of a set of recombinant inbred lines and
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genotype information for the same lines. It searches for an
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association between each expression trait and all genotypes and
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evaluates that association by a permutation test. For the permutation
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test, it performs only as many permutations as are necessary to define
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the empirical P-value to a reasonable precision. It also performs
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bootstrap resampling to estimate the confidence region for the
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location of a putative QTL.")
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(license license:gpl2+))))
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;; Reintroduced python2-gunicorn because we are running GN with python2
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;; right now. Please keep it until we migrate to Python3 fully!
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(define-public python-gunicorn-gn
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(package
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(name "python-gunicorn-gn")
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(version "19.9.0")
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(source
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(origin
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(method url-fetch)
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(uri (pypi-uri "gunicorn" version))
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(sha256
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(base32
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"1wzlf4xmn6qjirh5w81l6i6kqjnab1n1qqkh7zsj1yb6gh4n49ps"))))
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(build-system python-build-system)
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(inputs
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`(("python-mock" ,python-mock)))
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(arguments
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'(#:phases
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(modify-phases %standard-phases
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(add-after 'unpack 'loosen-verion-restrictions
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(lambda _
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(substitute* "requirements_test.txt"
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(("coverage.*") "coverage\n")
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(("pytest.*") "pytest\n")
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(("pytest-cov.*") "pytest-cov\n"))
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#t)))))
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(native-inputs
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`(("python-coverage" ,python-coverage)
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("python-pytest" ,python-pytest)
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("python-pytest-cov" ,python-pytest-cov)))
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(home-page "https://gunicorn.org")
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(synopsis "WSGI HTTP Server for UNIX")
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(description "Gunicorn 'Green Unicorn' is a Python WSGI HTTP Server for
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UNIX. It's a pre-fork worker model ported from Ruby's Unicorn project. The
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Gunicorn server is broadly compatible with various web frameworks, simply
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implemented, light on server resource usage, and fairly speedy.")
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(license license:expat)))
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(define-public python2-gunicorn-gn
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(package-with-python2 python-gunicorn-gn))
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(define-public rust-qtlreaper
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(let ((commit "2e7fed6d45b0b602d80fa2a55835f96ef1cba9e3")
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(revision "1"))
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(package
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(name "rust-qtlreaper")
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(version "0.1.4")
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(source
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(origin
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(method git-fetch)
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(uri (git-reference
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(url "https://github.com/chfi/rust-qtlreaper.git")
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(commit commit)))
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(file-name (git-file-name name version))
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(sha256
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(base32
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"0h70aalsplmc6xn1w7ha102n3bsi3gqkbnbrjvjm2za37c07gv0g"))))
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(build-system cargo-build-system)
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(arguments
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`(#:cargo-inputs
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(("rust-rand" ,rust-rand-0.6)
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("rust-structopt" ,rust-structopt-0.2)
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("rust-rayon" ,rust-rayon-1)
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("rust-serde" ,rust-serde-1)
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("rust-serde-json" ,rust-serde-json-1)
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("rust-ndarray" ,rust-ndarray-0.12))
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#:phases
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(modify-phases %standard-phases
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;; Test results vary based on the machine running them.
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(replace 'check
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(lambda _
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(or (assoc-ref %standard-phases 'check)
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(begin
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(substitute* "src/geneobject.rs"
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;; array![Genotype::Unk, Genotype::Unk, Genotype::Pat]
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(("0.3421367343627405") "0.3421367343627406")
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;; array![Genotype::Unk, Genotype::Unk, Genotype::Unk]
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(("-0.3223330030526561") "-0.32233300305265566"))
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(assoc-ref %standard-phases 'check)))
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#t)))))
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(home-page "https://github.com/chfi/rust-qtlreaper")
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(synopsis "Reimplementation of genenetwork/QTLReaper in Rust")
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(description "Reimplementation of genenetwork/QTLReaper in Rust")
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(license #f))))
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(define-public gfautil
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(package
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(name "gfautil")
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(version "0.1.0")
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(source
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(origin
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(method url-fetch)
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(uri (crate-uri "gfautil" version))
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(file-name
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(string-append name "-" version ".tar.gz"))
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(sha256
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(base32
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"0cgiis9v1nd4m7zxvgsz8jf8ijv4d8fa5wb7cpnjshksb8z7xh69"))))
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(build-system cargo-build-system)
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(arguments
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`(#:rust ,rust-1.42
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#:cargo-inputs
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(("rust-bstr" ,rust-bstr-0.2)
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("rust-clap" ,rust-clap-2)
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("rust-gfa" ,rust-gfa-0.6)
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("rust-handlegraph" ,rust-handlegraph-0.3)
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("rust-rayon" ,rust-rayon-1)
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("rust-serde" ,rust-serde-1)
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("rust-structopt" ,rust-structopt-0.3))))
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(home-page "https://github.com/chfi/rs-gfa-utils")
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(synopsis "Command line tools for working with GFA files")
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(description
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"This package provides command line tools for working with @acronym{GFA,
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Graphical Fragment Assembly} files and related formats.")
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(license license:expat)))
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(define-public python2-genenetwork2
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(let ((commit "1538ffd33af19e6ac922b4ee85fe701408968dfd"))
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(package
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(name "python2-genenetwork2")
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(version (string-append "2.11-guix-" (string-take commit 7) ))
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(source (origin
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(method git-fetch)
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(uri (git-reference
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(url "https://pjotrp@gitlab.com/genenetwork/gn2_diet.git")
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(commit commit)))
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(file-name (string-append name "-" version))
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(sha256
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(base32
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"0ji929xgzypyhchcfy9xa1sz04w322ibs2khc8s3qiddxjqdglrz"))))
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(propagated-inputs
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`(;; propagated for development purposes
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("python" ,python-2) ;; probably superfluous
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("coreutils" ,coreutils)
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("git" ,git)
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("which" ,which)
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("grep" ,grep)
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("r" ,r)
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("r-ctl" ,r-ctl)
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; ("r-phewas" ,r-phewas)
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("r-qtl" ,r-qtl)
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("r-wgcna" ,r-wgcna)
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("redis" ,redis)
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("mariadb" ,mariadb)
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("gemma" ,gemma-gn2)
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("gemma-wrapper" ,gemma-wrapper)
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; ("genenetwork2-files-small" ,genenetwork2-files-small)
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("plink-ng-gn" ,plink-ng-gn)
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; ("pylmm-gn2" ,pylmm-gn2)
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("rust-qtlreaper" ,rust-qtlreaper)
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("nginx" ,nginx)
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("python-twint" ,python-twint)
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("python2-coverage" ,python2-coverage)
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("python2-flask" ,python2-flask)
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("python2-gunicorn-gn" ,python2-gunicorn-gn)
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("python2-pillow" ,python2-pillow) ;; - for later!
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("python2-pil1" ,python2-pil1-gn)
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("python2-piddle-gn" ,python2-piddle-gn)
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("python2-cssselect" ,python2-cssselect)
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("python2-elasticsearch" ,python2-elasticsearch)
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; ("python2-htmlgen" ,python2-htmlgen)
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("python2-htmlgen-gn" ,python2-htmlgen-gn)
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("python2-jinja2" ,python2-jinja2)
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("python2-sqlalchemy" ,python2-sqlalchemy)
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("python2-flask-sqlalchemy" ,python2-flask-sqlalchemy)
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("python2-setuptools" ,python2-setuptools)
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("python2-scipy" ,python2-scipy)
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("python2-lxml" ,python2-lxml)
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("python2-mechanize" ,python2-mechanize)
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("python2-mock" ,python2-mock)
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("python2-mysqlclient" ,python2-mysqlclient)
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("python2-nose" ,python-nose2)
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("python2-numarray" ,python2-numarray)
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("python2-numpy" ,python2-numpy)
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("python2-pandas" ,python2-pandas)
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("python2-parallel" ,python2-parallel)
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("python2-parameterized" ,python2-parameterized)
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("python2-passlib" ,python2-passlib)
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("python2-redis" ,python2-redis)
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("python2-requests" ,python2-requests)
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("python2-rpy2" ,python2-rpy2)
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("python2-simplejson" ,python2-simplejson)
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("python2-pyyaml" ,python2-pyyaml)
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("python-unittest2" ,python-unittest2)
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("python2-xlsxwriter" ,python2-xlsxwriter)
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("python2-qtlreaper" ,python2-qtlreaper)
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;; All the external js dependencies
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("javascript-twitter-post-fetcher" ,javascript-twitter-post-fetcher)
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("javascript-cytoscape" ,javascript-cytoscape)
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("javascript-panzoom" ,javascript-cytoscape-panzoom)
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("javascript-qtip" ,javascript-cytoscape-qtip)
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("javascript-chroma" ,javascript-chroma)
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("javascript-d3-tip" ,javascript-d3-tip)
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("javascript-jscolor" ,javascript-jscolor)
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("javascript-colorbox" ,javascript-colorbox)
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("javascript-jszip" ,javascript-jszip)
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("js-jstat" ,js-jstat)
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("js-md5" ,js-md5)
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("js-parsley" ,js-parsley)
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("javascript-plotly" ,javascript-plotly)
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("javascript-typeahead" ,javascript-typeahead)
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("js-underscore" ,js-underscore)
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("js-smart-time-ago" ,js-smart-time-ago)
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("javascript-nouislider" ,javascript-nouislider)
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("javascript-purescript-genome-browser" ,javascript-purescript-genome-browser)
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("javascript-ckeditor" ,javascript-ckeditor)
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("javascript-datatables" ,javascript-datatables)
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("javascript-datatables-scroller" ,javascript-datatables-scroller)
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("javascript-datatables-buttons" ,javascript-datatables-buttons)
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("javascript-datatables-buttons-bootstrap" ,javascript-datatables-buttons-bootstrap)
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("javascript-datatables-plugins" ,javascript-datatables-plugins)
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("javascript-datatables-col-reorder" ,javascript-datatables-col-reorder)
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("javascript-datatables-col-resize" ,javascript-datatables-col-resize)
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("javascript-datatables-buttons-styles" ,javascript-datatables-buttons-styles)
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("javascript-shapiro-wilk" ,javascript-shapiro-wilk)
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("javascript-underscore-string" ,javascript-underscore-string)
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("javascript-qtip2" ,javascript-qtip2)
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("javascript-d3js" ,javascript-d3js)
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("javascript-nvd3" ,javascript-nvd3)
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("javascript-bootstrap" ,javascript-bootstrap)
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("javascript-jquery" ,javascript-jquery)
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("javascript-zxcvbn" ,javascript-zxcvbn)
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("javascript-jquery-ui" ,javascript-jquery-ui)
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("javascript-jquery-cookie" ,javascript-jquery-cookie)
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("javascript-font-awesome" ,javascript-font-awesome)))
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(inputs
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`(("javascript-colorbox" ,(package-source javascript-colorbox))))
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(build-system python-build-system)
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(arguments
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`(#:python ,python-2
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#:phases
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(modify-phases %standard-phases
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(delete 'reset-gzip-timestamps)
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(add-after 'unpack 'fix-paths-scripts
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(lambda _
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(substitute* "bin/genenetwork2"
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(("/usr/bin/env") (which "env"))
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(("python ") (string-append (which "python2") " "))
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(("readlink") (which "readlink"))
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(("dirname") (which "dirname"))
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(("basename") (which "basename"))
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(("cat") (which "cat"))
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(("echo") (which "echo"))
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(("redis-server") (which "redis-server"))
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(("git") (which "git"))
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(("grep") (which "grep"))
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(("rm") (which "rm"))
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(("which") (which "which")) ; three whiches in a row!
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)
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#t))
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(add-after 'unpack 'patch-javascript
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(lambda* (#:key inputs #:allow-other-keys)
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(let ((colorbox (assoc-ref inputs "javascript-colorbox"))
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(gn2 "/share/genenetwork2/javascript/"))
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(delete-file-recursively "wqflask/wqflask/static/packages/colorbox")
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(copy-recursively colorbox "wqflask/wqflask/static/packages/colorbox")
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#t)))
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(add-before 'install 'fix-paths
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(lambda* (#:key inputs #:allow-other-keys)
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(let* (
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; (datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2"))
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; (pylmmcmd (string-append (assoc-ref inputs "pylmm-gn2") "/bin/pylmm_redis"))
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(plink2cmd (string-append (assoc-ref inputs "plink-ng-gn") "/bin/plink2"))
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(gemmacmd (string-append (assoc-ref inputs "gemma") "/bin/gemma"))
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)
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(substitute* '("etc/default_settings.py")
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; (("^GENENETWORK_FILES +=.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" ))
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; (("^PYLMM_COMMAND =.*") (string-append "PYLMM_COMMAND = \"" pylmmcmd "\"\n" ))
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(("^PLINK_COMMAND =.*") (string-append "PLINK_COMMAND = \"" plink2cmd "\"\n" ))
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(("^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+))))
|
|
|
|
(define-public genenetwork3
|
|
(let ((commit "7d22039c2ae0aef6abc575008f11b95e555e3e9a"))
|
|
(package
|
|
(name "genenetwork3")
|
|
(version (string-append "0.0.1-guix-" (string-take commit 7)))
|
|
(source
|
|
(origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/genenetwork/genenetwork3.git")
|
|
(commit commit)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"19xs9yjv2qldyjkhw2v8dxw5r5gvm2vchcbfqrxi13qgvdidx65f"))))
|
|
(propagated-inputs `(("coreutils" ,coreutils)
|
|
("gemma-wrapper" ,gemma-wrapper)
|
|
("python" ,python-wrapper)
|
|
("python-bcrypt" ,python-bcrypt)
|
|
("python-flask" ,python-flask)
|
|
("python-ipfshttpclient" ,python-ipfshttpclient)
|
|
("python-mypy" ,python-mypy)
|
|
("python-mypy-extensions" ,python-mypy-extensions)
|
|
("python-mysqlclient" ,python-mysqlclient)
|
|
("python-numpy" ,python-numpy)
|
|
("python-pylint" ,python-pylint)
|
|
("python-redis" ,python-redis)
|
|
("python-requests" ,python-requests)
|
|
("python-scipy" ,python-scipy)
|
|
("python-sqlalchemy-stubs"
|
|
,python-sqlalchemy-stubs)
|
|
("r-optparse" ,r-optparse)
|
|
("r-qtl" ,r-qtl)
|
|
("r-stringi" ,r-stringi)))
|
|
(build-system python-build-system)
|
|
(home-page "https://github.com/genenetwork/genenetwork3")
|
|
(synopsis "GeneNetwork3 API for data science and machine learning.")
|
|
(description "GeneNetwork3 API for data science and machine learning.")
|
|
(license license:agpl3+))))
|
|
|
|
(define-public genenetwork2
|
|
(let ((commit "84cbf35adbb15c79638372d108308edb05f12683"))
|
|
(package
|
|
(inherit python2-genenetwork2)
|
|
(name "genenetwork2")
|
|
(version (string-append "3.11-guix-" (string-take commit 7) ))
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/genenetwork/genenetwork2.git")
|
|
(commit commit)))
|
|
(file-name (string-append name "-" version))
|
|
(sha256
|
|
(base32
|
|
"1402g129ghfh0xwfxjj1i7gbib2yl9rahf55caj7b1psy24ys87x"))))
|
|
(native-inputs
|
|
`(("graphviz" ,graphviz)))
|
|
(propagated-inputs
|
|
(let ((inputs (package-propagated-inputs python2-genenetwork2)))
|
|
`(,@(fold
|
|
alist-delete inputs
|
|
(map car
|
|
(filter (lambda (x)
|
|
(let ((name (car x)))
|
|
(or (string-prefix? "python2" name)
|
|
(string-prefix? "python-2" name)
|
|
(string=? "python" name))))
|
|
inputs)))
|
|
("genenetwork3" ,genenetwork3)
|
|
("parallel" ,parallel) ;; GNU parallel
|
|
("python" ,python-wrapper)
|
|
("python-pillow" ,python-pillow)
|
|
("python-coverage" ,python-coverage)
|
|
("python-configparser" ,python-configparser) ;; maintenance/scripts
|
|
("python-flask" ,python-flask)
|
|
("gunicorn" ,gunicorn)
|
|
("python-autopep8" ,python-autopep8)
|
|
("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)
|
|
("python-mypy" ,python-mypy)
|
|
("python-numpy" ,python-numpy)
|
|
("python-pandas" ,python-pandas)
|
|
("python-parameterized" ,python-parameterized)
|
|
("python-passlib" ,python-passlib)
|
|
("python-pylint" ,python-pylint)
|
|
("python-redis" ,python-redis)
|
|
("python-requests" ,python-requests)
|
|
("python-simplejson" ,python-simplejson)
|
|
("python-pyyaml" ,python-pyyaml)
|
|
("python-markdown" ,python-markdown)
|
|
("python-rdflib" ,python-rdflib)
|
|
;; TODO: Get rid of Python R bindings
|
|
("python-rpy2" ,python-rpy2-next)
|
|
("python-beautifulsoup4" ,python-beautifulsoup4)
|
|
;; Disable for now. Build fails on Penguin2
|
|
;; ("python-flask-socketio" ,python-flask-socketio)
|
|
("python-xlsxwriter" ,python-xlsxwriter))))
|
|
(arguments
|
|
(let ((python (specification->package "python-wrapper"))
|
|
(args (package-arguments python2-genenetwork2)))
|
|
(substitute-keyword-arguments args
|
|
((#:python _) python)
|
|
((#:phases phases)
|
|
`(modify-phases ,phases
|
|
(add-after 'unpack 'fix-paths-scripts
|
|
(lambda _
|
|
(substitute* "bin/genenetwork2"
|
|
(("/usr/bin/env") (which "env"))
|
|
(("python ") (string-append (which "python3") " "))
|
|
(("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")))
|
|
#t))
|
|
(add-after 'install 'generate-graph
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(call-with-output-file
|
|
(string-append
|
|
(assoc-ref outputs "out")
|
|
"/lib/python3.8/site-packages"
|
|
"/wqflask/dependency-graph.html")
|
|
(lambda (port)
|
|
(format
|
|
port "~a"
|
|
,(call-with-output-string
|
|
(lambda (p)
|
|
(with-output-to-port p
|
|
(lambda ()
|
|
(run-with-store
|
|
(open-connection)
|
|
(export-graph
|
|
(list this-package)
|
|
p
|
|
#:node-type %package-node-type
|
|
#:backend %d3js-backend)))))))))))
|
|
(add-after 'install 'generate-dag-svg-file
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(let* ((output-dir
|
|
(string-append
|
|
(assoc-ref outputs "out")
|
|
"/lib/python3.8/site-packages/wqflask/"))
|
|
(dot-file
|
|
(string-append
|
|
output-dir
|
|
"dependency-graph.dot"))
|
|
(svg-file
|
|
(string-append
|
|
output-dir
|
|
"dependency-graph.svg")))
|
|
(begin
|
|
(call-with-output-file
|
|
dot-file
|
|
(lambda (port)
|
|
(format
|
|
port "~a"
|
|
,(call-with-output-string
|
|
(lambda (p)
|
|
(with-output-to-port p
|
|
(lambda ()
|
|
(run-with-store
|
|
(open-connection)
|
|
(export-graph
|
|
(list this-package)
|
|
p
|
|
#:node-type %package-node-type
|
|
#:backend %graphviz-backend)))))))))
|
|
(invoke "dot" "-Tsvg" "-o" svg-file dot-file)))))
|
|
(add-after 'install 'generate-dependency-file
|
|
(lambda* (#:key inputs outputs #:allow-other-keys)
|
|
(call-with-output-file
|
|
(string-append
|
|
(assoc-ref outputs "out")
|
|
"/lib/python3.8/site-packages"
|
|
"/wqflask/DEPENDENCIES.md")
|
|
(lambda (port)
|
|
(format
|
|
port "
|
|
#### System Inputs (generated from ~a package defined in ~a)
|
|
|Name | Description |
|
|
|-----|-------------|
|
|
~a
|
|
"
|
|
,(package-name this-package)
|
|
(string-append
|
|
"[genenetwork.scm]"
|
|
"(http://git.genenetwork.org/"
|
|
"guix-bioinformatics/guix-bioinformatics"
|
|
"/src/branch/master/gn/packages/"
|
|
"genenetwork.scm)")
|
|
,(apply
|
|
string-append
|
|
(map
|
|
(lambda (input)
|
|
(let* ((pkg (cadr input))
|
|
(name (package-name pkg))
|
|
(version (package-version pkg))
|
|
(home-page (package-home-page pkg))
|
|
(description (package-synopsis pkg)))
|
|
(string-append
|
|
"| **[" name "](" home-page ")** v"
|
|
version"| "
|
|
description " |\n")))
|
|
(package-propagated-inputs this-package))))))))))))))))
|
|
|
|
;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip
|
|
;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x
|
|
|
|
(define-public genenetwork2-files-small
|
|
(let ((pfff "xx"))
|
|
(package
|
|
(name "genenetwork2-files-small")
|
|
(version "1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4")
|
|
(file-name (string-append name "-" pfff))
|
|
(sha256
|
|
(base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj"))))
|
|
(build-system trivial-build-system)
|
|
(native-inputs `(("lz4" ,lz4)
|
|
("tar" ,tar)
|
|
("source" ,source)))
|
|
|
|
(arguments
|
|
`(#:modules ((guix build utils))
|
|
#:builder
|
|
(let* ((out (assoc-ref %outputs "out"))
|
|
(name "gn2_data_s")
|
|
(tarfn (string-append name ".tar"))
|
|
(targetdir (string-append out "/share/genenetwork2/")))
|
|
(begin
|
|
(use-modules (guix build utils))
|
|
(let ((source (assoc-ref %build-inputs "source"))
|
|
(lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4"))
|
|
(tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar")))
|
|
(and
|
|
(zero? (system* lz4unpack source "-d" tarfn))
|
|
(zero? (system* tar "xf" tarfn))
|
|
(mkdir-p targetdir)
|
|
(copy-recursively name targetdir)))))))
|
|
(home-page "http://genenetwork.org/")
|
|
(synopsis "Small file archive to run on genenetwork")
|
|
(description "Genenetwork genotype and mapping files.")
|
|
(license license:agpl3+))))
|
|
|
|
(define-public genenetwork2-database-small
|
|
(let ((md5 "93e745e9c"))
|
|
(package
|
|
(name "genenetwork2-database-small")
|
|
(version "1.0")
|
|
(source
|
|
(origin
|
|
(method url-fetch)
|
|
(uri "http://files.genenetwork.org/raw_database/db_webqtl_s.zip")
|
|
(file-name (string-append name "-" md5))
|
|
(sha256
|
|
(base32 "0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x"))))
|
|
(build-system trivial-build-system)
|
|
(native-inputs `(("unzip" ,unzip)
|
|
("source" ,source)))
|
|
|
|
(arguments
|
|
`(#:modules ((guix build utils))
|
|
#:builder (begin
|
|
(use-modules (guix build utils))
|
|
(let ((source (assoc-ref %build-inputs "source"))
|
|
(unzip (string-append (assoc-ref %build-inputs "unzip") "/bin/unzip")))
|
|
(and (mkdir "db")
|
|
(zero? (system* unzip source "-d" "db"))
|
|
(chdir "db"))))))
|
|
(home-page "http://genenetwork.org/")
|
|
(synopsis "Small database to run on genenetwork")
|
|
(description "Genenetwork installation + database.")
|
|
(license license:agpl3+))))
|
|
|
|
|
|
|
|
(define-public python-reaper
|
|
(let ((commit "63391333a6619771277bfffa9bd9d33811fa0d28"))
|
|
(package
|
|
(name "python-reaper")
|
|
(version (string-append "0.0.1-"
|
|
(string-take commit 7)))
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/fredmanglis/reaper.git")
|
|
(commit commit)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"1rq2qn0vrqd8k676yy8drm0zxzkj065ywhxjl0j1n2r25zifay7r"))))
|
|
(build-system python-build-system)
|
|
(arguments
|
|
`(#:tests? #f))
|
|
(home-page "https://github.com/fredmanglis/reaper")
|
|
(synopsis "Parser for .geno files")
|
|
(description "Parser for .geno files. It replaces the Python2 library
|
|
written in C")
|
|
(license license:agpl3+))))
|
|
|
|
|
|
(define-public genenetwork1
|
|
(let ((commit "acf65ac9ae4be395c07c1629758f7408bf4eab5f") ; June 3, 2020
|
|
(revision "2"))
|
|
(package
|
|
(name "genenetwork1")
|
|
(version (git-version "0.0.0" revision commit))
|
|
(source (origin
|
|
(method git-fetch)
|
|
(uri (git-reference
|
|
(url "https://github.com/genenetwork/genenetwork1.git")
|
|
(commit commit)))
|
|
(file-name (git-file-name name version))
|
|
(sha256
|
|
(base32
|
|
"0xmmmjyvh80yd8b0cjrwpdmxl8k9zj5ly65r2g9aygx74njsp4fi"))))
|
|
(build-system gnu-build-system)
|
|
(native-inputs
|
|
`(("ghostscript" ,ghostscript)
|
|
("graphviz" ,graphviz)
|
|
("wget" ,wget)))
|
|
(propagated-inputs
|
|
`(("python" ,python-2.4)
|
|
("httpd-with-mod-python" ,httpd22-with-mod-python)
|
|
("python-direct" ,python24-direct)
|
|
("python-htmlgen-GN1" ,python24-htmlgen-GN1)
|
|
("python-json-GN1" ,python24-json-GN1)
|
|
("python-mysqlclient" ,python24-mysqlclient)
|
|
("python-numarray" ,python24-numarray)
|
|
("python-piddle" ,python24-piddle)
|
|
("python-pp-GN1" ,python24-pp-GN1)
|
|
("python-pyx" ,python24-pyx)
|
|
("python-pyxlwriter" ,python24-pyxlwriter)
|
|
("python-qtlreaper" ,python24-qtlreaper)
|
|
("python-rpy2" ,python24-rpy2)
|
|
("python-svg-GN1" ,python24-svg-GN1)))
|
|
(arguments
|
|
`(#:tests? #f ; no tests
|
|
#:phases
|
|
(modify-phases %standard-phases
|
|
(delete 'configure)
|
|
(delete 'build)
|
|
(add-after 'patch-generated-file-shebangs 'patch-more-files
|
|
(lambda* (#:key inputs #:allow-other-keys)
|
|
(let ((piddle (assoc-ref inputs "python-piddle")))
|
|
(substitute* "web/webqtl/networkGraph/networkGraphUtils.py"
|
|
(("/usr/local/bin/neato") (which "neato"))
|
|
(("/usr/local/bin/circo") (which "circo"))
|
|
(("/usr/local/bin/twopi") (which "twopi"))
|
|
(("/usr/local/bin/fdp") (which "fdp"))
|
|
(("ps2pdf") (which "ps2pdf")))
|
|
(substitute* "web/webqtl/maintainance/addRif.py"
|
|
(("rm ") (string-append (which "rm") " "))
|
|
(("wget ") (string-append (which "wget") " "))
|
|
(("gunzip") (which "gunzip")))
|
|
(substitute* "web/webqtl/misc/editHtmlPage.py"
|
|
(("/bin/cp") (which "cp")))
|
|
(substitute* "web/webqtl/geneWiki/AddGeneRIFPage.py"
|
|
(("touch") (which "touch")))
|
|
(substitute* '("web/webqtl/maintainance/addRif.py"
|
|
"web/webqtl/networkGraph/networkGraphPage.py"
|
|
"web/webqtl/utility/svg.py")
|
|
(("/usr/bin/(env )?python") (which "python")))
|
|
(substitute* "web/webqtl/base/webqtlConfigLocal.py"
|
|
(("PythonPath.*")
|
|
(string-append "PythonPath = '" (which "python") "'\n"))
|
|
(("PIDDLE_FONT_PATH.*/lib")
|
|
(string-append "PIDDLE_FONT_PATH = '" piddle "/lib"))))
|
|
#t))
|
|
(add-after 'patch-generated-file-shebangs 'changes-for-deployed-service
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(let ((out (assoc-ref outputs "out")))
|
|
(substitute* "web/webqtl/base/webqtlConfigLocal.py"
|
|
;; Where GN1 is located: (GNROOT)
|
|
(("/gnshare/gn") out)
|
|
;; Where the database is located: (sql_host)
|
|
(("tux01.uthsc.edu") "127.0.0.1"))
|
|
(substitute* '("web/webqtl/maintainance/QTL_Reaper_cal_lrs.py")
|
|
(("128\\.169\\.5\\.59") "localhost"))
|
|
;; This directory (TMPDIR) is expected to be writable by apache.
|
|
;; /tmp is private inside the container.
|
|
(symlink "/tmp" "web/tmp")
|
|
;; IMGDIR is expected to be writable.
|
|
(symlink "/tmp" "web/image")
|
|
(system "chmod 0777 web/tmp")
|
|
;; More writable locations:
|
|
(substitute* (list "web/webqtl/collection/ExportSelectionDetailInfoPage.py"
|
|
"web/webqtl/pairScan/DirectPlotPage.py"
|
|
"web/webqtl/updateTrait/DataUpdatePage.py"
|
|
"web/webqtl/utility/Plot.py")
|
|
(("/gnshare/gn/web/debug_file.txt") "/tmp/debug_file.txt"))
|
|
;; We mount the genotypes folder (GENODIR) in the OS-config and
|
|
;; provide the symlink to that location from the package.
|
|
;; And now the directory is magically available!
|
|
(symlink "/gnshare/gn/web/genotypes" "web/genotypes")
|
|
(substitute* "web/webqtl/base/webqtlConfig.py"
|
|
(("http://www.genenetwork.org") "http://gn1-test.genenetwork.org"))
|
|
;; Inside the gn1 container, there's some conflict when
|
|
;; importing the user module, therefore, as a hack, rename
|
|
;; user to useralt
|
|
(mkdir "web/webqtl/useralt")
|
|
(copy-recursively "web/webqtl/user" "web/webqtl/useralt")
|
|
(substitute* '("web/webqtl/main.py")
|
|
(("from user import") "from useralt import"))
|
|
#t)))
|
|
(add-after 'unpack 'use-local-links
|
|
(lambda _
|
|
(substitute* '("web/javascript/menu_items.js"
|
|
"web/webqtl/maintainance/updateMenuJS.py")
|
|
(("http://(www|gn1).genenetwork.org") ""))
|
|
|
|
;; Move this file out of the way while patching files.
|
|
(rename-file "web/infoshare/manager/MDB-Free/index.html"
|
|
"web/infoshare/manager/MDB-Free/index.htm")
|
|
(substitute* (cons*
|
|
"web/webqtl/base/indexBody.py"
|
|
"web/webqtl/submitTrait/BatchSubmitPage.py"
|
|
(find-files "web" "\\.html"))
|
|
((".*base href.*") "")
|
|
(("(HREF|href)=\\\"http://(www.)?genenetwork.org")
|
|
"href=\""))
|
|
;; Move this file back to its original location.
|
|
(rename-file "web/infoshare/manager/MDB-Free/index.htm"
|
|
"web/infoshare/manager/MDB-Free/index.html")
|
|
|
|
(substitute* (cons*
|
|
"web/humanCross.html"
|
|
"web/webqtl/base/indexBody.py"
|
|
"web/whats_new.html"
|
|
(find-files "web/dbdoc" "\\.html"))
|
|
(("src=\\\"http://www.genenetwork.org") "src=\""))
|
|
#t))
|
|
(replace 'install
|
|
(lambda* (#:key outputs #:allow-other-keys)
|
|
(copy-recursively "." (assoc-ref outputs "out"))
|
|
#t)))))
|
|
(home-page "http://www.genenetwork.org/webqtl/main.py")
|
|
(synopsis
|
|
"Combined database and data analysis software resource for systems genetics")
|
|
(description "GeneNetwork is a group of linked data sets and tools used to
|
|
study complex networks of genes, molecules, and higher order gene function and
|
|
phenotypes. GeneNetwork combines more than 25 years of legacy data generated by
|
|
hundreds of scientists together with sequence data (SNPs) and massive
|
|
transcriptome data sets (expression genetic or eQTL data sets). The
|
|
@dfn{quantitative trait locus} (QTL) mapping module that is built into GN is
|
|
optimized for fast on-line analysis of traits that are controlled by
|
|
combinations of gene
|
|
variants and environmental factors. GeneNetwork can be used to study humans,
|
|
mice (BXD, AXB, LXS, etc.), rats (HXB), Drosophila, and plant species (barley
|
|
and Arabidopsis). Most of these population data sets are linked with dense
|
|
genetic maps (genotypes) that can be used to locate the genetic modifiers that
|
|
cause differences in expression and phenotypes, including disease susceptibility.")
|
|
(license license:agpl3+))))
|