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-rw-r--r--gnu/packages/bioinformatics.scm58
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)