From: "Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
To: 48862@debbugs.gnu.org
Cc: rekado@elephly.net,
"Mădălin Ionel Patrașcu" <madalinionel.patrascu@mdc-berlin.de>
Subject: [bug#48862] [PATCH] gnu: python-hic2cool: Update to 0.8.3.
Date: Sun, 6 Jun 2021 07:14:07 +0200 [thread overview]
Message-ID: <20210606051407.6535-1-madalinionel.patrascu@mdc-berlin.de> (raw)
* gnu/packages/bioinformatics.scm (python-hic2cool): Update to 0.8.3.
---
gnu/packages/bioinformatics.scm | 28 ++++++++++++++++++++++------
1 file changed, 22 insertions(+), 6 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dab097381a..66e69ff2c8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -11892,18 +11892,34 @@ pyGenomeTracks can make plots with or without Hi-C data.")
(define-public python-hic2cool
(package
(name "python-hic2cool")
- (version "0.4.2")
+ (version "0.8.3")
+ ;; pypi sources do not contain the test_data directory and no test can be
+ ;; run
(source
(origin
- (method url-fetch)
- (uri (pypi-uri "hic2cool" version))
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/4dn-dcic/hic2cool")
+ (commit version)))
+ (file-name (git-file-name name version))
(sha256
(base32
- "0xy6mhfns2lzib1kcr6419jjp6pmh0qx8z8na55lmiwn0ds8q9cl"))))
+ "0dlnf0qfcp4jrc1nyya32a035c13xicyq16bwfnwhbb9s47mz7gl"))))
(build-system python-build-system)
- (arguments '(#:tests? #f)) ; no tests included
+ (arguments
+ `(#:phases
+ (modify-phases %standard-phases
+ ;;two of the test-data files need to be writable
+ (add-after 'unpack 'patch-test-data
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (chmod "test_data/hic2cool_0.4.2_single_res.cool" #o600)
+ (chmod "test_data/hic2cool_0.7.0_multi_res.mcool" #o600))))))
(propagated-inputs
- `(("python-cooler" ,python-cooler)))
+ `(("python-cooler" ,python-cooler)
+ ("python-h5py" ,python-h5py)
+ ("python-numpy" ,python-numpy)
+ ("python-pandas" ,python-pandas)
+ ("python-scipy" ,python-scipy)))
(home-page "https://github.com/4dn-dcic/hic2cool")
(synopsis "Converter for .hic and .cool files")
(description
--
2.31.1
next reply other threads:[~2021-06-06 5:15 UTC|newest]
Thread overview: 4+ messages / expand[flat|nested] mbox.gz Atom feed top
2021-06-06 5:14 Mădălin Ionel Patrașcu [this message]
[not found] ` <handler.48862.B.162295649121933.ack@debbugs.gnu.org>
2021-06-06 7:31 ` [bug#48862] [ext] bug#48862: Acknowledgement ([PATCH] gnu: python-hic2cool: Update to 0.8.3.) Mădălin Ionel Patrașcu
2021-06-06 7:32 ` [bug#48862] [PATCH v2] gnu: python-hic2cool: Update to 0.8.3 Mădălin Ionel Patrașcu
2021-06-07 7:40 ` bug#48862: [PATCH] " Efraim Flashner
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