diff options
author | Ricardo Wurmus <rekado@elephly.net> | 2023-05-26 14:35:54 +0200 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2023-05-26 14:36:14 +0200 |
commit | 60b71b0db4ab690817df78f711cc3267419ad6c0 (patch) | |
tree | d54d1dd5a3844fc9408f9e55e2b0ae1c735c35d2 /gnu/packages/bioinformatics.scm | |
parent | bb6ddc269f776e0c3dc739fb9f49a4c048db3b44 (diff) |
gnu: Add python-gseapy.
* gnu/packages/bioinformatics.scm (python-gseapy): New variable.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r-- | gnu/packages/bioinformatics.scm | 108 |
1 files changed, 108 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 0cd4ea7b32..8698bf7563 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -20103,6 +20103,114 @@ handling."))) "BĂogo is a bioinformatics library for the Go language.") (license license:bsd-3))) +(define-public python-gseapy + (package + (name "python-gseapy") + (version "1.0.4") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/zqfang/GSEApy") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "06gh09dwwj2xr5zx8i41smy8arx2pw7rll7sk50np28z419bnyz9")))) + (build-system cargo-build-system) + (arguments + (list + #:install-source? #false + #:features '(list "extension-module") + #:cargo-test-flags '(list "--features=extension-module") + #:cargo-inputs + `(("rust-csv" ,rust-csv-1) + ("rust-itertools" ,rust-itertools-0.10) + ("rust-pyo3" ,rust-pyo3-0.16) + ("rust-rand" ,rust-rand-0.8) + ("rust-rayon" ,rust-rayon-1) + ("rust-serde" ,rust-serde-1)) + #:imported-modules + (append %cargo-build-system-modules + %pyproject-build-system-modules) + #:modules + '((guix build cargo-build-system) + ((guix build pyproject-build-system) #:prefix py:) + (guix build utils)) + #:phases + #~(modify-phases %standard-phases + (add-after 'install 'prepare-python-module + (lambda _ + ;; We don't use maturin, nor do we use setuptools-rust. + (delete-file "pyproject.toml") + (call-with-output-file "pyproject.toml" + (lambda (port) + (format port "\ +[build-system] +build-backend = 'setuptools.build_meta' +requires = ['setuptools'] +"))) + (delete-file "setup.py") + (call-with-output-file "setup.cfg" + (lambda (port) + (format port "\ +[metadata] +name = gseapy +version = ~a + +[options] +packages = find: + +[options.packages.find] +exclude = + src + docs + tests + Cargo.toml +" #$version))))) + ;; We delete the Cargo checks but run the Python tests later. + ;; See https://github.com/zqfang/GSEApy/issues/207 + (delete 'check) + (add-after 'prepare-python-module 'enable-bytecode-determinism + (assoc-ref py:%standard-phases 'enable-bytecode-determinism)) + (add-after 'enable-bytecode-determinism 'build-python-module + (assoc-ref py:%standard-phases 'build)) + (add-after 'build-python-module 'install-python-module + (assoc-ref py:%standard-phases 'install)) + (add-after 'install-python-module 'install-python-library + (lambda _ + (let ((site (string-append #$output "/lib/python" + #$(version-major+minor + (package-version python)) + "/site-packages"))) + (mkdir-p site) + (copy-file "target/release/libgse.so" + (string-append site "/gseapy/gse.so"))))) + (add-after 'install-python-library 'add-install-to-pythonpath + (assoc-ref py:%standard-phases 'add-install-to-pythonpath)) + (add-after 'add-install-to-pythonpath 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" "tests" + ;; These tests need access to the internet + "-k" "not test_enrichr and not test_prerank"))))))) + (inputs + (list python-wrapper)) + (native-inputs + (list python-pytest)) + (propagated-inputs + (list python-numpy + python-scipy + python-pandas + python-matplotlib + python-requests)) + (home-page "https://github.com/zqfang/gseapy") + (synopsis "Gene Set Enrichment Analysis in Python") + (description "GSEApy is a Python/Rust implementation for GSEA and wrapper +for Enrichr. GSEApy can be used for RNA-seq, ChIP-seq, Microarray data. It +can be used for convenient GO enrichment and to produce publication quality +figures in Python.") + (license license:bsd-3))) + ;;; ;;; Avoid adding new packages to the end of this file. To reduce the chances ;;; of a merge conflict, place them above by existing packages with similar |