guix_mirror_bot pushed a commit to branch master
in repository guix.
commit b68eb98be030d26cef50bd2ae4c337b9db22557e
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Thu Oct 30 10:21:36 2025 +0000
gnu: python-cmseq: Fix build.
* gnu/packages/bioinformatics.scm (python-bcbio-gff/biopython-1.73):
Rename variable to python-bcbio-gff-for-python-cmseq and pin to 0.6.9
version which is the last one compatible with python-biopython-1.73.
(python-cmseq)[propagated-inputs]: Remove
python-bcbio-gff/biopython-1.73; add python-bcbio-gff-for-python-cmseq.
[native-inputs]: Add python-setuptools.
Change-Id: Id7c37f8f34058648506645ce07c2a89dfcea2067
---
gnu/packages/bioinformatics.scm | 17 +++++++++++++++--
1 file changed, 15 insertions(+), 2 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c0c0ae3200..2a1fc96868 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2204,10 +2204,21 @@ Format (GFF) with Biopython integration.")
'((upstream-name . "bcbio-gff")))
(license (license:non-copyleft "http://www.biopython.org/DIST/LICENSE";))))
-(define-public python-bcbio-gff/biopython-1.73
+(define-public python-bcbio-gff-for-python-cmseq
(hidden-package
(package
(inherit python-bcbio-gff)
+ (name "python-bcbio-gff")
+ (version "0.6.9")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/chapmanb/bcbb";)
+ (commit (string-append "bcbio-gff-v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "131hiir94jkm9jj2wfpybwndgzn8k0zc1ji1qjn5cz7w48x3ri13"))))
(propagated-inputs
(modify-inputs (package-propagated-inputs python-bcbio-gff)
(replace "python-biopython" python-biopython-1.73))))))
@@ -2671,9 +2682,11 @@ cell types and subtypes.")
(substitute* "cmseq/cmseq.py"
(("'samtools'")
(string-append "'" (search-input-file inputs "/bin/samtools")
"'"))))))))
+ (native-inputs
+ (list python-setuptools))
(inputs (list samtools))
(propagated-inputs
- (list python-bcbio-gff/biopython-1.73
+ (list python-bcbio-gff-for-python-cmseq
python-biopython-1.73
python-numpy
python-pandas
