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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 59 |
1 files changed, 59 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3801e827c6..a49d8455ce 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4699,6 +4699,65 @@ self-contained (one single directory) and the platform is written in Python, in a modular way.") (license license:gpl3))) +(define-public python-presto + (package + (name "python-presto") + (version "0.7.6") + (home-page "https://github.com/immcantation/presto") + (source + (origin + (method git-fetch) + (uri (git-reference + (url home-page) + (commit version))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "1mcngwrxiw8r1j26r5crf7j0dscvhg3b8g1is3j3vq5jpnyn8jmz")))) + (build-system pyproject-build-system) + (propagated-inputs + (list muscle + python-biopython + python-numpy + python-pandas + python-pyyaml + python-scipy + vsearch)) + (native-inputs + (list python-pytest + python-setuptools + python-wheel)) + (arguments + (list + #:build-backend "setuptools.build_meta" + #:test-flags + ;; FileNotFoundError: [Errno 2] No such file or directory: 'cd-hit-est' + '(list "--ignore=tests/test_ClusterSets.py"))) + (synopsis "The REpertoire Sequencing TOolkit") + (description "Presto is a python toolkit for processing raw reads from +high-throughput sequencing of B cell and T cell repertoires.") + (license license:agpl3))) + +(define-public python-fastalite + (package + (name "python-fastalite") + (version "0.3") + (source + (origin + (method url-fetch) + (uri (pypi-uri "fastalite" version)) + (sha256 + (base32 + "1qli6pxp77i9xn2wfciq2zaxhl82bdxb33cpzqzj1z25yd036wqj")))) + (build-system python-build-system) + (arguments + `(#:tests? #f)) ; Test data is not distributed. + (home-page "https://github.com/nhoffman/fastalite") + (synopsis "Simplest possible FASTA parser") + (description "This library implements a FASTA and a FASTQ parser without +relying on a complex dependency tree.") + (license license:expat))) + (define-public biosoup (package (name "biosoup") |