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authorEfraim Flashner2023-03-22 14:22:33 +0200
committerEfraim Flashner2023-03-22 14:22:33 +0200
commitadd8bb0bdf3797704a30095ef21058b11778bc27 (patch)
tree3bef32b2ab4b2e76cecf2346013196248a26f1c6
parent3cddd10e7b3a52d1d3f8411417e3b59a1ae558c9 (diff)
downloadguix-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.scm13
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