guix_mirror_bot pushed a commit to branch python-team
in repository guix.
commit 6db404202921bb1a82327a2cea1d85e5577ef62d
Author: Sharlatan Hellseher <[email protected]>
AuthorDate: Sat Dec 13 08:43:37 2025 +0000
gnu: cpat: Update to 3.0.5.
* gnu/packages/bioinformatics.scm (cpat): Update to 3.0.5.
[source]: Switch to git-fetch providing test data.
<snippet>: Remove as no longer required.
[phases]{check}: Rework test steps, run cpat directly with correct
inputs.
[native-inputs]: Remove python-wheel.
Change-Id: I813cdf4aff2e75b855fc75237d9103f34aff45f2
---
gnu/packages/bioinformatics.scm | 47 +++++++++++++++++++++--------------------
1 file changed, 24 insertions(+), 23 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 25e65c7947..e3d237789b 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -701,37 +701,38 @@ for many other tasks.")
(define-public cpat
(package
(name "cpat")
- (version "3.0.4")
- (source (origin
- (method url-fetch)
- (uri (pypi-uri "CPAT" version))
- (sha256
- (base32
- "0dfrwwbhv1n4nh2a903d1qfb30fgxgya89sa70aci3wzf8h2z0vd"))
- (modules '((guix build utils)))
- (snippet
- '(for-each delete-file-recursively
- (list ".eggs"
- "lib/__pycache__/"
- "lib/cpmodule/__pycache__/")))))
+ (version "3.0.5")
+ (source
+ (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/liguowang/cpat";)
+ (commit (string-append "v" version))))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32 "13l2bxaxn4bf7fglx2vnsxfjzvav96d9v78gzwx71sp7wgsjwz9w"))))
(build-system pyproject-build-system)
(arguments
(list
#:phases
- '(modify-phases %standard-phases
- (replace 'check
- (lambda* (#:key tests? #:allow-other-keys)
- (when tests?
- (with-directory-excursion "test"
- ;; There is no test4.fa
- (substitute* "test.sh"
- ((".*-g test4.fa.*") ""))
- (invoke "bash" "test.sh"))))))))
+ #~(modify-phases %standard-phases
+ (replace 'check
+ ;; Working test steps from <test_files/test.sh> file.
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (with-directory-excursion "test_files"
+ (system* "gunzip" "Human_test_coding_mRNA.fa.gz")
+ (invoke "cpat" "--hex=Human_Hexamer.tsv"
+ "--logitModel=Human_logitModel.RData"
+ "--top-orf=5"
+ "--outfile=out5"
+ "--gene=Human_test_coding_mRNA.fa"
+ "--antisense"))))))))
(propagated-inputs
(list python-numpy python-pysam))
(inputs
(list r-minimal))
- (native-inputs (list python-setuptools python-wheel))
+ (native-inputs (list python-setuptools))
(home-page "https://wlcb.oit.uci.edu/cpat/";)
(synopsis "Alignment-free distinction between coding and noncoding RNA")
(description
