guix_mirror_bot pushed a commit to branch next-master
in repository guix.
commit 9fd8ba94fad8d09088a0018b3233c16113a17ef3
Author: Hugo Buddelmeijer <[email protected]>
AuthorDate: Thu Oct 30 22:05:49 2025 +0100
gnu: python-scanrbp: Include data in package.
* gnu/packages/bioinformatics.scm (python-scanrbp): Fix build and include
data.
[native-inputs]: Remove python-wheel.
<#:phases>: Add 'patchpath and 'copy-data phases. Replace 'check phase.
Change-Id: Ie61792f696f59383789cac89bf9f354f0ce1d188
Signed-off-by: Sharlatan Hellseher <[email protected]>
---
gnu/packages/bioinformatics.scm | 57 ++++++++++++++++++++++++++++++++++++-----
1 file changed, 50 insertions(+), 7 deletions(-)
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index dd8e35719c..f75d7451a0 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -4696,19 +4696,62 @@ into separate processes; and more.")
(build-system pyproject-build-system)
(arguments
(list
- #:tests? #f ; There are none.
+ ;; There are no tests in repository. However, running the example from
the
+ ;; README is added as a test below. But that fails, because python-pybio
+ ;; needs to access the internet.
+ ;; TODO: Fix python-pybio to not (or optionally) require internet,
+ ;; and then enable the tests here.
+ #:tests? #f
#:phases
#~(modify-phases %standard-phases
- (add-before 'check 'set-HOME
- (lambda _ (setenv "HOME" "/tmp")))
- (add-before 'check 'copy-data
- (lambda _
- (let ((data-dir (string-append (getenv "HOME") "/scanRBP_data"))
+ ;; Normally, importing scanRBP for the first time will first create
+ ;; configuration file `~/.scanRBP` with a `data_folder` specified as
+ ;; `~/scanRBP_data/`. Then `data.tar.gz` is downloaded from the
github
+ ;; project and placed into this directory.
+ ;;
+ ;; Instead of doing all that, all internet access can be prevented:
+ ;; - copy the `data.tar.gz` tarball directly to the store,
+ ;; - refer to that directory in the example configuration file,
+ ;; - set the configuration file path to that example file.
+ (add-before 'build 'patchpath
+ (lambda* (#:key inputs outputs #:allow-other-keys)
+ (let ((data-dir (string-append (assoc-ref outputs "out")
+ "/share/scanRBP_data")))
+ (substitute* "scanRBP/scanRBP.config.example"
+ (("~/scanRBP_data") data-dir))
+ (substitute* "scanRBP/config/__init__.py"
+ (("config_fname = .*")
+ (string-append
+ "config_fname = \""
+ (site-packages inputs outputs)
+ "/scanRBP/scanRBP.config.example\"\n"))))))
+ (add-before 'install 'copy-data
+ (lambda* (#:key outputs #:allow-other-keys)
+ (let ((data-dir (string-append (assoc-ref outputs "out")
+ "/share/scanRBP_data"))
(data-file "data/data.tar.gz"))
+ ;; Copy the tarball. The tarball is unpacked when files are
+ ;; imported in the [sanity-]check phase.
(mkdir-p data-dir)
(copy-file
data-file
- (string-append data-dir "/" (basename data-file)))))))))
+ (string-append data-dir "/" (basename data-file))))))
+ (add-before 'check 'set-HOME
+ ;; Set the HOME directory to make python-pybio work.
+ (lambda _ (setenv "HOME" "/tmp")))
+ (replace 'check
+ ;; Run example from the README.
+ ;; The test currently fails (and is therefore disabled), because
+ ;; python-pybio currently needs to access the internet.
+ ;; TODO: Verify results?
+ (lambda* (#:key tests? #:allow-other-keys)
+ (when tests?
+ (invoke
+ "scanRBP"
+
"AAAGCGGCGACTTATTATATCCCCATATATTATATCTTCTTCTCTTATATATAAACCAGAGATAGATGTGTGTGGTGG"
+ "example1"
+ "-heatmap"
+ "example1")))))))
(propagated-inputs
(list python-biopython
python-matplotlib
