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| author | Efraim Flashner | 2023-03-22 14:22:33 +0200 |
|---|---|---|
| committer | Efraim Flashner | 2023-03-22 14:22:33 +0200 |
| commit | add8bb0bdf3797704a30095ef21058b11778bc27 (patch) | |
| tree | 3bef32b2ab4b2e76cecf2346013196248a26f1c6 | |
| parent | 3cddd10e7b3a52d1d3f8411417e3b59a1ae558c9 (diff) | |
| download | guix-bioinformatics-add8bb0bdf3797704a30095ef21058b11778bc27.tar.gz | |
bh20-seq-resource: Patch reference to minimap2.
* gn/packages/bioinformatics.scm (bh20-seq-resource)[arguments]: Add
phase to hardcode path to minimap2.
[inputs]: Add minimap2.
| -rw-r--r-- | gn/packages/bioinformatics.scm | 13 |
1 files changed, 12 insertions, 1 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 48f1c40..b94f537 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -1812,7 +1812,16 @@ suitable for long reads, but works also well with short reads.") (build-system python-build-system) (arguments (list - #:tests? #f)) ; Tests can't find pytest + #:tests? #f ; Tests can't find pytest + #:phases + #~(modify-phases %standard-phases + (add-after 'unpack 'patch-program-calls + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "bh20sequploader/qc_fasta.py" + (("\"minimap2\"") + (string-append "\"" (search-input-file + inputs "/bin/minimap2") + "\"")))))))) (propagated-inputs (list python-arvados-python-client python-schema-salad @@ -1829,6 +1838,8 @@ suitable for long reads, but works also well with short reads.") ;; and for the service python gunicorn)) + (inputs + (list minimap2)) (native-inputs (list python-pytest-4 ; < 6 python-pytest-runner-4)) ; < 5 |