diff options
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 248 |
1 files changed, 205 insertions, 43 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 6c6ff3e25a..207f3c3d28 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) @@ -846,7 +847,7 @@ intended to behave exactly the same as the original BWK awk.") (define-public python-cellbender (package (name "python-cellbender") - (version "0.2.1") + (version "0.2.2") (source (origin (method git-fetch) @@ -856,8 +857,8 @@ intended to behave exactly the same as the original BWK awk.") (file-name (git-file-name name version)) (sha256 (base32 - "1zav2q8nnss80i25y06fccagkvrqsy7lpylsl4dxv4qkj8p4fnv3")))) - (build-system python-build-system) + "12q22va7rbc3sx9ygc6p6hh6xw9wbqjmhba5h5gb836p5xplj5fa")))) + (build-system pyproject-build-system) (arguments (list #:tests? #false)) ;there are none (propagated-inputs @@ -884,14 +885,14 @@ from high-throughput single-cell RNA sequencing (scRNA-seq) data.") (define-public python-htsget (package (name "python-htsget") - (version "0.2.5") + (version "0.2.6") (source (origin (method url-fetch) (uri (pypi-uri "htsget" version)) (sha256 (base32 - "0ic07q85vhw9djf23k57b21my7i5xp400m8gfqgr5gcryqvdr0yk")))) - (build-system python-build-system) + "111q4pzkav26aa3hkgh948wqlyrq7dq6sjml9z63n3blw8s6b0c4")))) + (build-system pyproject-build-system) (native-inputs (list python-setuptools-scm)) (propagated-inputs @@ -913,11 +914,12 @@ servers supporting the protocol.") (sha256 (base32 "18rhzk08d3rpxhi5xh6pqg64x6v5q3daw6y3v54k85v4swncjrwj")))) - (build-system python-build-system) + (build-system pyproject-build-system) (arguments `(#:modules ((srfi srfi-26) (guix build utils) - (guix build python-build-system)) + (guix build python-build-system) + (guix build pyproject-build-system)) ;; See https://github.com/daler/pybedtools/issues/192 #:phases (modify-phases %standard-phases @@ -977,7 +979,7 @@ which are widely used for genomic interval manipulation or \"genome algebra\". pybedtools extends BEDTools by offering feature-level manipulations from with Python.") ;; pypi lists GPLv2 in the PKG-INFO and website, but was relicensed in - ;; version 0.9.0 and the LICENSE.txt is consistant with the source code. + ;; version 0.9.0 and the LICENSE.txt is consistent with the source code. ;; ;; pybedtools/include/gzstream.cpp and pybedtools/include/gzstream.h are ;; licensed lgpl2.1+ @@ -1031,7 +1033,7 @@ use-case, we encourage users to compose functions to achieve their goals.") (define-public python-biom-format (package (name "python-biom-format") - (version "2.1.10") + (version "2.1.12") (source (origin (method git-fetch) @@ -1043,25 +1045,22 @@ use-case, we encourage users to compose functions to achieve their goals.") (file-name (git-file-name name version)) (sha256 (base32 - "0i62j6ksmp78ap2dnl969gq6vprc3q87zc8ksj9if8g2603iq6i8")) + "06x2d8fv80jp86kd66fm3ragmxrpa2j0lzsbm337ziqjnpsdwc0f")) (modules '((guix build utils))) ;; Delete generated C files. (snippet '(for-each delete-file (find-files "." "\\.c"))))) (build-system python-build-system) (arguments - `(#:phases - (modify-phases %standard-phases + (list + #:phases + '(modify-phases %standard-phases (add-after 'unpack 'use-cython (lambda _ (setenv "USE_CYTHON" "1"))) - (add-after 'unpack 'relax - (lambda _ - (substitute* "setup.py" - (("pytest < 5.3.4") "pytest")))) (add-after 'unpack 'disable-broken-tests (lambda _ - (substitute* "biom/tests/test_cli/test_validate_table.py" - (("^(.+)def test_invalid_hdf5" m indent) + (substitute* "biom/tests/test_util.py" + (("^(.+)def test_biom_open_hdf5_no_h5py" m indent) (string-append indent "@npt.dec.skipif(True, msg='Guix')\n" m))) @@ -1072,13 +1071,14 @@ use-case, we encourage users to compose functions to achieve their goals.") m)))))))) (propagated-inputs (list python-anndata - python-numpy - python-scipy + python-click python-flake8 python-future - python-click python-h5py - python-pandas)) + python-numpy + python-pandas + python-scikit-bio + python-scipy)) (native-inputs (list python-cython python-pytest python-pytest-cov python-nose)) (home-page "http://www.biom-format.org") @@ -1093,42 +1093,45 @@ e.g. microbiome samples, genomes, metagenomes.") (define-public python-pairtools (package (name "python-pairtools") - (version "0.3.0") + (version "1.0.2") (source (origin (method git-fetch) (uri (git-reference - (url "https://github.com/mirnylab/pairtools") + (url "https://github.com/open2c/pairtools") (commit (string-append "v" version)))) (file-name (git-file-name name version)) (sha256 (base32 - "0gr8y13q7sd6yai6df4aavl2470n1f9s3cib6r473z4hr8hcbwmc")))) + "0xn4cg4jq3rfn42h8rfwg0k6xkvihjrv32gwldb9y0jp05lzw9cs")))) (build-system python-build-system) (arguments `(#:phases (modify-phases %standard-phases (add-after 'unpack 'fix-references (lambda _ - (substitute* '("pairtools/pairtools_merge.py" - "pairtools/pairtools_sort.py") - (("/bin/bash") (which "bash"))) - #t)) + (substitute* '("pairtools/cli/header.py" + "pairtools/cli/merge.py" + "pairtools/cli/sort.py") + (("/bin/bash") (which "bash"))))) (replace 'check - (lambda* (#:key inputs outputs #:allow-other-keys) - (add-installed-pythonpath inputs outputs) - (with-directory-excursion "/tmp" - (invoke "pytest" "-v"))))))) + (lambda* (#:key tests? #:allow-other-keys) + (when tests? + (with-directory-excursion "/tmp" + (invoke "pytest" "-v")))))))) (native-inputs - (list python-cython python-nose python-pytest)) - (inputs - `(("python" ,python-wrapper))) + (list python-cython python-pytest)) (propagated-inputs (list htslib ; for bgzip, looked up in PATH samtools ; looked up in PATH lz4 ; for lz4c + python-bioframe python-click - python-numpy)) - (home-page "https://github.com/mirnylab/pairtools") + python-numpy + python-pandas + python-pysam + python-pyyaml + python-scipy)) + (home-page "https://github.com/open2c/pairtools") (synopsis "Process mapped Hi-C data") (description "Pairtools is a simple and fast command-line framework to process sequencing data from a Hi-C experiment. Process pair-end sequence @@ -1173,8 +1176,7 @@ alignments and perform the following operations: (package-inputs this-package))))))) `(#:phases (modify-phases %standard-phases - (add-after - 'install 'wrap-programs + (add-after 'install 'wrap-programs (lambda* (#:key outputs #:allow-other-keys) ;; Make sure all executables in "bin" find the required Perl ;; modules at runtime. As the PERL5LIB variable contains also @@ -1191,8 +1193,7 @@ alignments and perform the following operations: (for-each (lambda (file) (wrap-program file `("PERL5LIB" ":" prefix (,path)))) - (find-files bin "\\.pl$")) - #t))))))) + (find-files bin "\\.pl$"))))))))) (inputs (list perl-module-build perl-data-stag perl-libwww perl-uri)) (native-inputs @@ -2973,6 +2974,71 @@ generation, and transformation to RDF. Salad provides a bridge between document and record oriented data modeling and the Semantic Web.") (license license:asl2.0))) +(define-public python-scikit-bio + (package + (name "python-scikit-bio") + (version "0.5.7") + (source (origin + (method url-fetch) + (uri (pypi-uri "scikit-bio" version)) + (sha256 + (base32 + "1a8xbp3vrw8wfpm3pa2nb4rcar0643iqnb043ifwqbqyc86clhv3")))) + (build-system pyproject-build-system) + (arguments + (list + #:phases + '(modify-phases %standard-phases + ;; See https://github.com/biocore/scikit-bio/pull/1826 + (add-after 'unpack 'compatibility + (lambda _ + (substitute* "skbio/sequence/tests/test_sequence.py" + (("def test_concat_strict_many") + "def _do_not_test_concat_strict_many")) + (substitute* "skbio/stats/distance/_mantel.py" + (("from scipy.stats import PearsonRConstantInputWarning") + "from scipy.stats import ConstantInputWarning") + (("from scipy.stats import PearsonRNearConstantInputWarning") + "from scipy.stats import NearConstantInputWarning") + (("from scipy.stats import SpearmanRConstantInputWarning") "") + (("warnings.warn\\(PearsonRConstantInputWarning\\(\\)\\)") + "warnings.warn(ConstantInputWarning())") + (("warnings.warn\\(PearsonRNearConstantInputWarning\\(\\)\\)") + "warnings.warn(NearConstantInputWarning())") + (("warnings.warn\\(SpearmanRConstantInputWarning\\(\\)\\)") + "warnings.warn(ConstantInputWarning())")) + (substitute* "skbio/diversity/alpha/tests/test_base.py" + (("self.assertEqual\\(pielou_e") + "self.assertAlmostEqual(pielou_e")))) + (add-before 'check 'build-extensions + (lambda _ + ;; Cython extensions have to be built before running the tests. + (invoke "python3" "setup.py" "build_ext" "--inplace"))) + (replace 'check + (lambda* (#:key tests? #:allow-other-keys) + (when tests? (invoke "python3" "-m" "skbio.test"))))))) + (propagated-inputs + (list python-cachecontrol + python-decorator + python-h5py + python-hdmedians + python-ipython + python-lockfile + python-matplotlib + python-natsort + python-numpy + python-pandas + python-scikit-learn + python-scipy)) + (native-inputs + (list python-coverage python-pytest)) + (home-page "https://scikit-bio.org") + (synopsis "Data structures, algorithms and educational resources for bioinformatics") + (description + "This package provides data structures, algorithms and educational +resources for bioinformatics.") + (license license:bsd-3))) + (define-public cwltool (package (name "cwltool") @@ -10601,6 +10667,102 @@ 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") |