[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]
branch master updated: gnu: Add python-pairtools.
From: |
guix-commits |
Subject: |
branch master updated: gnu: Add python-pairtools. |
Date: |
Wed, 03 Jun 2020 09:05:32 -0400 |
This is an automated email from the git hooks/post-receive script.
rekado pushed a commit to branch master
in repository guix.
The following commit(s) were added to refs/heads/master by this push:
new 2f49007 gnu: Add python-pairtools.
2f49007 is described below
commit 2f49007dd076b14feb40d7c3331dee3e737265c8
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Wed Jun 3 15:01:19 2020 +0200
gnu: Add python-pairtools.
* gnu/packages/bioinformatics.scm (python-pairtools): New variable.
---
gnu/packages/bioinformatics.scm | 58 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 58 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 7ef55a2..8d1adaf 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)
[Prev in Thread] |
Current Thread |
[Next in Thread] |
- branch master updated: gnu: Add python-pairtools.,
guix-commits <=