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author | Ricardo Wurmus <rekado@elephly.net> | 2022-08-23 13:30:52 +0200 |
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committer | Ricardo Wurmus <rekado@elephly.net> | 2022-08-23 13:30:52 +0200 |
commit | d26b29d263e2a3ce5c7ef446f4bfcdcec75ab39f (patch) | |
tree | a027935860b0a466bd4aa53c7e2b04b61f2db703 | |
parent | 01dfcad225a2eeca469bfdd665e01c7fb2d28941 (diff) | |
download | guix-d26b29d263e2a3ce5c7ef446f4bfcdcec75ab39f.tar.gz |
gnu: Add flair.
* gnu/packages/bioinformatics.scm (flair): New variable.
-rw-r--r-- | gnu/packages/bioinformatics.scm | 49 |
1 files changed, 49 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 23a0fcd8b2..2bae609614 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -16456,6 +16456,55 @@ module capable of computing base-level alignments for very large sequences.") (home-page "https://github.com/ekg/wfmash") (license license:expat))) +(define-public flair + (package + (name "flair") + (version "1.6.2") + (source + (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/BrooksLabUCSC/flair") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "106swb2q7l20ki58fca1hg95q5f79bgp9gjb0clr2243ycrzyxf8")))) + (build-system python-build-system) + (arguments + (list + #:tests? #false ;there are none + #:phases + #~(modify-phases %standard-phases + ;; TODO: implement as a feature of python-build-system (PEP-621, + ;; PEP-631, PEP-660) + (replace 'build + (lambda _ + (setenv "SETUPTOOLS_SCM_PRETEND_VERSION" #$version) + ;; ZIP does not support timestamps before 1980. + (setenv "SOURCE_DATE_EPOCH" "315532800") + (invoke "python" "-m" "build" "--wheel" "--no-isolation" "."))) + (replace 'install + (lambda _ + (apply invoke "pip" "--no-cache-dir" "--no-input" + "install" "--no-deps" "--prefix" #$output + (find-files "dist" "\\.whl$"))))))) + (propagated-inputs + (list python-mappy + python-ncls + python-pybedtools + python-pysam + python-tqdm)) + (native-inputs + (list python-pypa-build python-setuptools)) + (home-page "https://flair.readthedocs.io/en/latest/") + (synopsis "Full-length alternative isoform analysis of RNA") + (description "This package implements FLAIR (Full-Length Alternative +Isoform analysis of RNA) for the correction, isoform definition, and +alternative splicing analysis of noisy reads. FLAIR has primarily been used +for nanopore cDNA, native RNA, and PacBio sequencing reads.") + (license license:bsd-3))) + (define-public go-github-com-biogo-graph (package (name "go-github-com-biogo-graph") |