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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 76 |
1 files changed, 76 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index e48b340a3a..241b99f23d 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -86,6 +86,7 @@ #:use-module (gnu packages documentation) #:use-module (gnu packages databases) #:use-module (gnu packages datastructures) + #:use-module (gnu packages digest) #:use-module (gnu packages dlang) #:use-module (gnu packages file) #:use-module (gnu packages flex) @@ -5291,6 +5292,81 @@ way to download and use genomic data. This includes All with sensible, yet controllable defaults.") (license license:expat))) +(define-public python-gimmemotifs + (package + (name "python-gimmemotifs") + (version "0.18.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vanheeringen-lab/gimmemotifs/") + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0jxr8884k7lic88vhr35l59q5qlpm64p4sv3xfq3l4y41ansh2z0")) + (modules '((guix build utils))) + ;; Delete included third-party binaries + (snippet + '(delete-file-recursively "src")))) + (build-system pyproject-build-system) + (arguments + (list + #:test-flags + ;; A lot of the tests depend on a wide range of external tools. + '(list "--ignore=test/test_02_config.py" + "--ignore=test/test_06_moap.py" + "--ignore=test/test_06_stats.py" + "--ignore=test/test_08_denovo.py" + "--ignore=test/test_08_maelstrom.py" + "--ignore=test/test_08_prediction.py" + "--ignore=test/test_09_cli.py" + "-k" + (string-append "not test_tool" + ;; not needed + " and not test_black_formatting" + " and not test_flake8_formatting" + " and not test_isort_formatting")) + #:phases + '(modify-phases %standard-phases + (add-after 'unpack 'do-not-copy-binaries + (lambda _ + (substitute* "setup.py" + (("^cmdclass\\[\"build_py.*") "")))) + (add-after 'unpack 'set-HOME + (lambda _ (setenv "HOME" "/tmp"))) + ;; This fails because there is no configuration file to load. + (delete 'sanity-check)))) + (propagated-inputs (list python-biofluff + python-configparser + python-diskcache + python-feather-format + python-genomepy + python-iteround + python-jinja2 + python-logomaker + python-loguru + python-matplotlib + python-numpy + python-pandas + python-pybedtools + python-pysam + python-qnorm + python-scikit-learn + python-scipy + python-seaborn + python-setuptools + python-statsmodels + python-tqdm + python-xdg + python-xxhash)) + (native-inputs (list python-pytest)) + (home-page "https://github.com/vanheeringen-lab/gimmemotifs/") + (synopsis "GimmeMotifs is a motif prediction pipeline.") + (description "GimmeMotifs is a suite of motif tools, including a motif +prediction pipeline for ChIP-seq experiments.") + (license license:expat))) + (define-public java-htsjdk (package (name "java-htsjdk") |