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04/09: gnu: clipper: Update to 2.0.1.
From: |
guix-commits |
Subject: |
04/09: gnu: clipper: Update to 2.0.1. |
Date: |
Tue, 7 Dec 2021 17:52:13 -0500 (EST) |
rekado pushed a commit to branch core-updates-frozen
in repository guix.
commit 6eecbfb9ac63f0d0fcb31ec5e92f3aad357fe5a5
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Tue Dec 7 19:40:28 2021 +0100
gnu: clipper: Update to 2.0.1.
* gnu/packages/bioinformatics.scm (clipper): Update to 2.0.1.
[source]: Add snippet to remove pre-compiled files.
[arguments]: Disable tests, delete 'sanity-check phase, and add
'use-python3-for-cython phase.
---
gnu/packages/bioinformatics.scm | 36 +++++++++++++++++++++++++++++-------
1 file changed, 29 insertions(+), 7 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c7413bd..b6970eb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2628,7 +2628,7 @@ databases.")
(define-public clipper
(package
(name "clipper")
- (version "2.0")
+ (version "2.0.1")
(source (origin
(method git-fetch)
(uri (git-reference
@@ -2637,10 +2637,16 @@ databases.")
(file-name (git-file-name name version))
(sha256
(base32
- "1bcag4lb5bkzsj2vg7lrq24aw6yfgq275ifrbhd82l7kqgbbjbkv"))))
+ "0508rgnfjk5ar5d1mjbjyrnarv4kw9ksq0m3jw2bmgabmb5v6ikk"))
+ (modules '((guix build utils)))
+ (snippet
+ '(begin
+ ;; Delete pre-compiled files.
+ (delete-file "clipper/src/peaks.so")))))
(build-system python-build-system)
(arguments
- `(#:phases
+ `(#:tests? #false
+ #:phases
(modify-phases %standard-phases
(add-before 'reset-gzip-timestamps 'make-files-writable
(lambda* (#:key outputs #:allow-other-keys)
@@ -2648,14 +2654,30 @@ databases.")
;; 'reset-gzip-timestamps' phase can do its work.
(let ((out (assoc-ref outputs "out")))
(for-each make-file-writable
- (find-files out "\\.gz$"))
- #t)))
+ (find-files out "\\.gz$")))))
+ (add-after 'unpack 'use-python3-for-cython
+ (lambda _
+ (substitute* "setup.py"
+ (("^setup")
+ "\
+peaks.cython_directives = {'language_level': '3'}
+readsToWiggle.cython_directives = {'language_level': '3'}
+setup"))))
(add-after 'unpack 'disable-nondeterministic-test
(lambda _
;; This test fails/succeeds non-deterministically.
(substitute* "clipper/test/test_call_peak.py"
- (("test_get_FDR_cutoff_mean") "_test_get_FDR_cutoff_mean"))
- #t)))))
+ (("test_get_FDR_cutoff_mean") "_test_get_FDR_cutoff_mean"))))
+ ;; This doesn't work because "usage" is executed, and that calls
+ ;; exit(8).
+ (replace 'check
+ (lambda* (#:key tests? inputs outputs #:allow-other-keys)
+ (when tests?
+ (add-installed-pythonpath inputs outputs)
+ (with-directory-excursion "clipper/test"
+ (invoke "python" "-m" "unittest")))))
+ ;; This is not a library
+ (delete 'sanity-check))))
(inputs
`(("htseq" ,htseq)
("python-pybedtools" ,python-pybedtools)
- branch core-updates-frozen updated (8dcf062 -> 5fb1ba8), guix-commits, 2021/12/07
- 01/09: gnu: Add pbcopper., guix-commits, 2021/12/07
- 03/09: gnu: pbbam: Update to 1.7.0., guix-commits, 2021/12/07
- 08/09: gnu: blasr: Update to 5.3.5., guix-commits, 2021/12/07
- 02/09: gnu: bwa-pssm: Fix build., guix-commits, 2021/12/07
- 04/09: gnu: clipper: Update to 2.0.1.,
guix-commits <=
- 05/09: gnu: htseq: Update to 0.12.3., guix-commits, 2021/12/07
- 06/09: gnu: blasr-libcpp: Update to 5.3.5., guix-commits, 2021/12/07
- 07/09: gnu: blasr: Remove trailing #T., guix-commits, 2021/12/07
- 09/09: gnu: newick-utils: Pass -fcommon to compiler., guix-commits, 2021/12/07