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12/12: gnu: Add python-gimmemotifs.
From: |
guix-commits |
Subject: |
12/12: gnu: Add python-gimmemotifs. |
Date: |
Fri, 5 May 2023 09:40:28 -0400 (EDT) |
rekado pushed a commit to branch master
in repository guix.
commit dc8b3ebe5d4ba2a39c12f62d836963ffee1e4b47
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Fri May 5 15:38:52 2023 +0200
gnu: Add python-gimmemotifs.
* gnu/packages/bioinformatics.scm (python-gimmemotifs): New variable.
---
gnu/packages/bioinformatics.scm | 76 +++++++++++++++++++++++++++++++++++++++++
1 file changed, 76 insertions(+)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index e48b340a3a..241b99f23d 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -86,6 +86,7 @@
#:use-module (gnu packages documentation)
#:use-module (gnu packages databases)
#:use-module (gnu packages datastructures)
+ #:use-module (gnu packages digest)
#:use-module (gnu packages dlang)
#:use-module (gnu packages file)
#:use-module (gnu packages flex)
@@ -5291,6 +5292,81 @@ way to download and use genomic data. This includes
All with sensible, yet controllable defaults.")
(license license:expat)))
+(define-public python-gimmemotifs
+ (package
+ (name "python-gimmemotifs")
+ (version "0.18.0")
+ (source (origin
+ (method git-fetch)
+ (uri (git-reference
+ (url "https://github.com/vanheeringen-lab/gimmemotifs/")
+ (commit version)))
+ (file-name (git-file-name name version))
+ (sha256
+ (base32
+ "0jxr8884k7lic88vhr35l59q5qlpm64p4sv3xfq3l4y41ansh2z0"))
+ (modules '((guix build utils)))
+ ;; Delete included third-party binaries
+ (snippet
+ '(delete-file-recursively "src"))))
+ (build-system pyproject-build-system)
+ (arguments
+ (list
+ #:test-flags
+ ;; A lot of the tests depend on a wide range of external tools.
+ '(list "--ignore=test/test_02_config.py"
+ "--ignore=test/test_06_moap.py"
+ "--ignore=test/test_06_stats.py"
+ "--ignore=test/test_08_denovo.py"
+ "--ignore=test/test_08_maelstrom.py"
+ "--ignore=test/test_08_prediction.py"
+ "--ignore=test/test_09_cli.py"
+ "-k"
+ (string-append "not test_tool"
+ ;; not needed
+ " and not test_black_formatting"
+ " and not test_flake8_formatting"
+ " and not test_isort_formatting"))
+ #:phases
+ '(modify-phases %standard-phases
+ (add-after 'unpack 'do-not-copy-binaries
+ (lambda _
+ (substitute* "setup.py"
+ (("^cmdclass\\[\"build_py.*") ""))))
+ (add-after 'unpack 'set-HOME
+ (lambda _ (setenv "HOME" "/tmp")))
+ ;; This fails because there is no configuration file to load.
+ (delete 'sanity-check))))
+ (propagated-inputs (list python-biofluff
+ python-configparser
+ python-diskcache
+ python-feather-format
+ python-genomepy
+ python-iteround
+ python-jinja2
+ python-logomaker
+ python-loguru
+ python-matplotlib
+ python-numpy
+ python-pandas
+ python-pybedtools
+ python-pysam
+ python-qnorm
+ python-scikit-learn
+ python-scipy
+ python-seaborn
+ python-setuptools
+ python-statsmodels
+ python-tqdm
+ python-xdg
+ python-xxhash))
+ (native-inputs (list python-pytest))
+ (home-page "https://github.com/vanheeringen-lab/gimmemotifs/")
+ (synopsis "GimmeMotifs is a motif prediction pipeline.")
+ (description "GimmeMotifs is a suite of motif tools, including a motif
+prediction pipeline for ChIP-seq experiments.")
+ (license license:expat)))
+
(define-public java-htsjdk
(package
(name "java-htsjdk")
- 04/12: gnu: Add python-mysql-connector-python., (continued)
- 04/12: gnu: Add python-mysql-connector-python., guix-commits, 2023/05/05
- 09/12: gnu: Add python-qnorm., guix-commits, 2023/05/05
- 11/12: gnu: Add python-norns., guix-commits, 2023/05/05
- 06/12: gnu: Add python-filelock-3.5., guix-commits, 2023/05/05
- 07/12: gnu: Add python-genomepy., guix-commits, 2023/05/05
- 08/12: gnu: Add python-biofluff., guix-commits, 2023/05/05
- 01/12: gnu: python-pyfaidx: Update to 0.7.2.1., guix-commits, 2023/05/05
- 02/12: gnu: Add python-palettable., guix-commits, 2023/05/05
- 05/12: gnu: Add python-logomaker., guix-commits, 2023/05/05
- 10/12: gnu: Add python-xdg., guix-commits, 2023/05/05
- 12/12: gnu: Add python-gimmemotifs.,
guix-commits <=