diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 97 |
1 files changed, 97 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6c6ff3e25a..c3cdbb9e66 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -57,6 +57,7 @@ #:use-module (guix build-system meson) #:use-module (guix build-system ocaml) #:use-module (guix build-system perl) + #:use-module (guix build-system pyproject) #:use-module (guix build-system python) #:use-module (guix build-system qt) #:use-module (guix build-system r) @@ -10601,6 +10602,102 @@ traditional read alignments) and massively-parallel stochastic collapsed variational inference.") (license license:gpl3+))) +(define-public python-fanc + (package + (name "python-fanc") + (version "0.9.25") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/vaquerizaslab/fanc") + ;; There are no tags. This commit corresponds to + ;; version 0.9.25. + (commit "e2205346c13ea5349681dff21adeb271d4ea5261"))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0rxq24p852iiayi0083fyigvc30as695rha71q6xd4s2ij1k9mqi")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (invoke "pytest" "-vv" + "-k" + ;; XXX: These all fail because they fail to read + ;; the included test_{cooler,juicer}.hic files. + (string-append "not test_edges_iter" + " and not test_get_edges_uncorrected" + " and not test_get_edges")))))))) + (propagated-inputs + (list python-biopython + python-cooler + python-deprecated + python-future + python-genomic-regions + python-gridmap + python-h5py + python-intervaltree + python-matplotlib + python-msgpack + python-msgpack-numpy + python-numpy + python-pandas + python-pillow + python-progressbar2 + python-pybedtools + python-pybigwig + python-pysam + python-pytest + python-pyyaml + python-scikit-image + python-scikit-learn + python-scipy + python-seaborn + python-tables)) + (native-inputs + (list python-cython)) + (home-page "https://github.com/vaquerizaslab/fanc") + (synopsis "Framework for the analysis of C-data") + (description + "FAN-C provides a pipeline for analysing Hi-C data starting at +mapped paired-end sequencing reads.") + (license license:gpl3+))) + +(define-public python-genomic-regions + (package + (name "python-genomic-regions") + (version "0.0.10") + (source (origin + (method url-fetch) + (uri (pypi-uri "genomic_regions" version)) + (sha256 + (base32 + "0hz811iyd1prml1r90qyzimmwyjwycwkjqw4vnl12bxy61rfzjz5")))) + (build-system pyproject-build-system) + (propagated-inputs + (list python-future + python-intervaltree + python-numpy + python-pandas + python-pybedtools + python-pybigwig + python-pytest + python-msgpack-numpy + python-cython + python-msgpack + python-pysam)) + (home-page "https://pypi.org/project/genomic-regions/") + (synopsis "Consistently handle genomic regions") + (description "This package aims to simplify working with genomic region / +interval data by providing a common interface that lets you access a wide +selection of file types and formats for handling genomic region data---all +using the same syntax.") + (license license:expat))) + (define-public python-loompy (package (name "python-loompy") |