rekado pushed a commit to branch master
in repository guix.
commit fadbc2d6602eeb0fac3aec6e1d057a9a9ac7d038
Author: Ricardo Wurmus <[email protected]>
AuthorDate: Wed Jan 15 21:19:03 2025 +0100
gnu: Deprecate fanc.
fanc is a duplicate of python-fanc.
* gnu/packages/bioinformatics.scm (fanc): Define as deprecated name for
python-fanc.
Change-Id: I28e330d9bfe64fd59b49001ecc56e2c6fd191b55
---
gnu/packages/bioinformatics.scm | 61 ++---------------------------------------
1 file changed, 3 insertions(+), 58 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 92eee018d8..0dca040570 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7508,64 +7508,6 @@ similarity of community members.")
Oxford Nanopore Technologies sequencing data.")
(license license:expat)))
-(define-public fanc
- (let ((commit "354401e52ba2320e6b1ba0d3b5aab3541d31c9f3")
- (revision "1"))
- (package
- (name "fanc")
- (version (git-version "0" revision commit))
- (source (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/vaquerizaslab/fanc.git";)
- (commit commit)))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0vp2cak5snla4j2q23d3ixx016bwzvxfiv4z6yp7anl0xaksd5bl"))))
- (build-system pyproject-build-system)
- (arguments
- (list
- #:test-flags
- '(list "-m" "not longrunning"
- ;; XXX: some of the tests here just take forever
- "--ignore=fanc/test/test_matrix.py")))
- (propagated-inputs
- (list python-biopython
- python-cooler
- python-deprecated
- python-future
- python-genomic-regions
- python-gridmap
- python-h5py
- python-imageio
- python-intervaltree
- python-matplotlib
- python-msgpack
- python-msgpack-numpy
- python-numpy
- python-pandas
- python-pillow
- python-progressbar2
- python-pybedtools
- python-pybigwig
- python-pysam
- python-pywavelets
- python-pyyaml
- python-scikit-image
- python-scikit-learn
- python-scipy
- python-seaborn
- python-tables
- python-tifffile))
- (native-inputs
- (list python-cython python-pytest))
- (home-page "https://github.com/vaquerizaslab/fanc";)
- (synopsis "Framework for the analysis of C-like data")
- (description "FAN-C provides a pipeline for analysing Hi-C data starting
-at mapped paired-end sequencing reads.")
- (license license:gpl3+))))
-
(define-public fasttree
(package
(name "fasttree")
@@ -16448,6 +16390,9 @@ lowly expressed transcripts.")
mapped paired-end sequencing reads.")
(license license:gpl3+)))
+(define-public fanc
+ (deprecated-package "fanc" python-fanc))
+
(define-public python-genomic-regions
(package
(name "python-genomic-regions")
