diff options
Diffstat (limited to 'gnu')
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 57 |
1 files changed, 50 insertions, 7 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 61834b46903..39acfd20a9a 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -4697,19 +4697,62 @@ 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 |