From add8bb0bdf3797704a30095ef21058b11778bc27 Mon Sep 17 00:00:00 2001 From: Efraim Flashner Date: Wed, 22 Mar 2023 14:22:33 +0200 Subject: 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. --- gn/packages/bioinformatics.scm | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) 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 -- cgit v1.2.3