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[bug#55424] [PATCH 017/602] gnu: Remove ribodiff.
From: |
Maxim Cournoyer |
Subject: |
[bug#55424] [PATCH 017/602] gnu: Remove ribodiff. |
Date: |
Sun, 15 May 2022 00:36:44 -0400 |
* gnu/packages/bioinformatics.scm (ribodiff): Delete variable.
---
gnu/packages/bioinformatics.scm | 46 ---------------------------------
1 file changed, 46 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index c754cdb176..902e65394d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -839,52 +839,6 @@ (define-public ribotaper
provides the Ribotaper pipeline.")
(license license:gpl3+)))
-(define-public ribodiff
- (package
- (name "ribodiff")
- (version "0.2.2")
- (source
- (origin
- (method git-fetch)
- (uri (git-reference
- (url "https://github.com/ratschlab/RiboDiff")
- (commit (string-append "v" version))))
- (file-name (git-file-name name version))
- (sha256
- (base32
- "0x75nlp7qnmm64jasbi6l21f2cy99r2cjyl6b4hr8zf2bq22drnz"))))
- (build-system python-build-system)
- (arguments
- `(#:python ,python-2
- #:phases
- (modify-phases %standard-phases
- ;; This test fails because of the matplotlib plotting backend.
- (add-after 'unpack 'disable-plot-test
- (lambda _
- (substitute* "src/ribodiff/functional_test_te.py"
- (("pl\\.make_plots\\(data, opts\\)") "#"))))
- ;; Generate an installable executable script wrapper.
- (add-after 'unpack 'patch-setup.py
- (lambda _
- (substitute* "setup.py"
- (("^(.*)packages=.*" line prefix)
- (string-append line "\n"
- prefix "scripts=['scripts/TE.py'],\n"))))))))
- (inputs
- (list python2-numpy python2-matplotlib python2-scipy
- python2-statsmodels))
- (native-inputs
- (list python2-mock python2-nose))
- (home-page "https://public.bmi.inf.ethz.ch/user/zhongy/RiboDiff/")
- (synopsis "Detect translation efficiency changes from ribosome footprints")
- (description "RiboDiff is a statistical tool that detects the protein
-translational efficiency change from Ribo-Seq (ribosome footprinting) and
-RNA-Seq data. It uses a generalized linear model to detect genes showing
-difference in translational profile taking mRNA abundance into account. It
-facilitates us to decipher the translational regulation that behave
-independently with transcriptional regulation.")
- (license license:gpl3+)))
-
(define-public bioawk
(package
(name "bioawk")
--
2.36.0
- [bug#55424] [PATCH 061/602] gnu: Remove ocrodjvu., (continued)
[bug#55424] [PATCH 058/602] gnu: Remove python2-hiredis., Maxim Cournoyer, 2022/05/15
[bug#55424] [PATCH 059/602] gnu: Remove python2-pytest-pep8., Maxim Cournoyer, 2022/05/15
[bug#55424] [PATCH 063/602] gnu: Remove python2-html5lib., Maxim Cournoyer, 2022/05/15
[bug#55424] [PATCH 068/602] gnu: Remove python2-pytest-warnings., Maxim Cournoyer, 2022/05/15
[bug#55424] [PATCH 065/602] gnu: Remove python2-pytest-cache., Maxim Cournoyer, 2022/05/15
[bug#55424] [PATCH 075/602] gnu: Remove lekha., Maxim Cournoyer, 2022/05/15
[bug#55424] [PATCH 023/602] gnu: Remove bamm., Maxim Cournoyer, 2022/05/15
[bug#55424] [PATCH 062/602] gnu: Remove python2-pandas., Maxim Cournoyer, 2022/05/15
[bug#55424] [PATCH 017/602] gnu: Remove ribodiff.,
Maxim Cournoyer <=
[bug#55424] [PATCH 013/602] gnu: Remove raul-devel., Maxim Cournoyer, 2022/05/15
[bug#55424] [PATCH 036/602] gnu: Remove python2-nose2., Maxim Cournoyer, 2022/05/15
[bug#55424] [PATCH 072/602] gnu: Remove omnitux., Maxim Cournoyer, 2022/05/15
[bug#55424] [PATCH 070/602] gnu: Remove python2-pickleshare., Maxim Cournoyer, 2022/05/15
[bug#55424] [PATCH 073/602] gnu: Remove childsplay., Maxim Cournoyer, 2022/05/15
[bug#55424] [PATCH 030/602] gnu: Remove python2-pbcore., Maxim Cournoyer, 2022/05/15
[bug#55424] [PATCH 066/602] gnu: Remove python2-fastlmm., Maxim Cournoyer, 2022/05/15
[bug#55424] [PATCH 078/602] gnu: Remove python2-keepkey., Maxim Cournoyer, 2022/05/15
[bug#55424] [PATCH 000/602] Purge Python 2 packages, Guillaume Le Vaillant, 2022/05/15