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| -rw-r--r-- | gnu/packages/bioinformatics.scm | 58 |
1 files changed, 58 insertions, 0 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 7ef55a25a3..8d1adafd7e 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -972,6 +972,64 @@ e.g. microbiome samples, genomes, metagenomes.") (("install_requires.append\\(\"pyqi\"\\)") "pass")) #t))))))))) +(define-public python-pairtools + (package + (name "python-pairtools") + (version "0.3.0") + (source (origin + (method git-fetch) + (uri (git-reference + (url "https://github.com/mirnylab/pairtools") + (commit (string-append "v" version)))) + (file-name (git-file-name name version)) + (sha256 + (base32 + "0gr8y13q7sd6yai6df4aavl2470n1f9s3cib6r473z4hr8hcbwmc")))) + (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)) + (replace 'check + (lambda* (#:key inputs outputs #:allow-other-keys) + (add-installed-pythonpath inputs outputs) + (with-directory-excursion "/tmp" + (invoke "pytest" "-v"))))))) + (native-inputs + `(("python-cython" ,python-cython) + ("python-nose" ,python-nose) + ("python-pytest" ,python-pytest))) + (inputs + `(("python" ,python-wrapper))) + (propagated-inputs + `(("htslib" ,htslib) ; for bgzip, looked up in PATH + ("samtools" ,samtools) ; looked up in PATH + ("lz4" ,lz4) ; for lz4c + ("python-click" ,python-click) + ("python-numpy" ,python-numpy))) + (home-page "https://github.com/mirnylab/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 +alignments and perform the following operations: + +@itemize +@item detect ligation junctions (a.k.a. Hi-C pairs) in aligned paired-end + sequences of Hi-C DNA molecules +@item sort @code{.pairs} files for downstream analyses +@item detect, tag and remove PCR/optical duplicates +@item generate extensive statistics of Hi-C datasets +@item select Hi-C pairs given flexibly defined criteria +@item restore @code{.sam} alignments from Hi-C pairs. +@end itemize +") + (license license:expat))) + (define-public bioperl-minimal (let* ((inputs `(("perl-module-build" ,perl-module-build) ("perl-data-stag" ,perl-data-stag) |