gnu: Add python-gseapy.
* gnu/packages/bioinformatics.scm (python-gseapy): New variable.
This commit is contained in:
Ricardo Wurmus
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1 changed files with 108 additions and 0 deletions
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@ -20103,6 +20103,114 @@ handling.")))
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"Bíogo is a bioinformatics library for the Go language.")
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"Bíogo is a bioinformatics library for the Go language.")
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(license license:bsd-3)))
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(license license:bsd-3)))
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(define-public python-gseapy
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(package
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(name "python-gseapy")
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(version "1.0.4")
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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/zqfang/GSEApy")
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(commit (string-append "v" version))))
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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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"06gh09dwwj2xr5zx8i41smy8arx2pw7rll7sk50np28z419bnyz9"))))
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(build-system cargo-build-system)
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(arguments
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(list
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#:install-source? #false
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#:features '(list "extension-module")
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#:cargo-test-flags '(list "--features=extension-module")
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#:cargo-inputs
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`(("rust-csv" ,rust-csv-1)
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("rust-itertools" ,rust-itertools-0.10)
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("rust-pyo3" ,rust-pyo3-0.16)
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("rust-rand" ,rust-rand-0.8)
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("rust-rayon" ,rust-rayon-1)
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("rust-serde" ,rust-serde-1))
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#:imported-modules
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(append %cargo-build-system-modules
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%pyproject-build-system-modules)
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#:modules
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'((guix build cargo-build-system)
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((guix build pyproject-build-system) #:prefix py:)
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(guix build utils))
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#:phases
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#~(modify-phases %standard-phases
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(add-after 'install 'prepare-python-module
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(lambda _
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;; We don't use maturin, nor do we use setuptools-rust.
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(delete-file "pyproject.toml")
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(call-with-output-file "pyproject.toml"
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(lambda (port)
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(format port "\
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[build-system]
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build-backend = 'setuptools.build_meta'
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requires = ['setuptools']
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")))
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(delete-file "setup.py")
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(call-with-output-file "setup.cfg"
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(lambda (port)
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(format port "\
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[metadata]
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name = gseapy
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version = ~a
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[options]
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packages = find:
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[options.packages.find]
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exclude =
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src
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docs
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tests
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Cargo.toml
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" #$version)))))
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;; We delete the Cargo checks but run the Python tests later.
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;; See https://github.com/zqfang/GSEApy/issues/207
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(delete 'check)
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(add-after 'prepare-python-module 'enable-bytecode-determinism
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(assoc-ref py:%standard-phases 'enable-bytecode-determinism))
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(add-after 'enable-bytecode-determinism 'build-python-module
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(assoc-ref py:%standard-phases 'build))
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(add-after 'build-python-module 'install-python-module
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(assoc-ref py:%standard-phases 'install))
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(add-after 'install-python-module 'install-python-library
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(lambda _
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(let ((site (string-append #$output "/lib/python"
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#$(version-major+minor
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(package-version python))
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"/site-packages")))
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(mkdir-p site)
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(copy-file "target/release/libgse.so"
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(string-append site "/gseapy/gse.so")))))
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(add-after 'install-python-library 'add-install-to-pythonpath
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(assoc-ref py:%standard-phases 'add-install-to-pythonpath))
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(add-after 'add-install-to-pythonpath 'check
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(lambda* (#:key tests? #:allow-other-keys)
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(when tests?
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(invoke "pytest" "-vv" "tests"
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;; These tests need access to the internet
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"-k" "not test_enrichr and not test_prerank")))))))
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(inputs
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(list python-wrapper))
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(native-inputs
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(list python-pytest))
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(propagated-inputs
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(list python-numpy
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python-scipy
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python-pandas
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python-matplotlib
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python-requests))
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(home-page "https://github.com/zqfang/gseapy")
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(synopsis "Gene Set Enrichment Analysis in Python")
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(description "GSEApy is a Python/Rust implementation for GSEA and wrapper
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for Enrichr. GSEApy can be used for RNA-seq, ChIP-seq, Microarray data. It
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can be used for convenient GO enrichment and to produce publication quality
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figures in Python.")
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(license license:bsd-3)))
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;;;
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;;;
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;;; Avoid adding new packages to the end of this file. To reduce the chances
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;;; Avoid adding new packages to the end of this file. To reduce the chances
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;;; of a merge conflict, place them above by existing packages with similar
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;;; of a merge conflict, place them above by existing packages with similar
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