From c4e5fabb6ef1a07967960f9b585847503cca0613 Mon Sep 17 00:00:00 2001 From: Ricardo Wurmus Date: Thu, 11 Nov 2021 14:44:37 +0000 Subject: gnu: ciri-long: Fix reference to ccs. * gnu/packages/bioinformatics.scm (ciri-long)[arguments]: Add build phase "fix-reference-to-ccs". [inputs]: Add circtools. --- gnu/packages/bioinformatics.scm | 17 ++++++++++++++--- 1 file changed, 14 insertions(+), 3 deletions(-) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 13bd7b5997..3455029ed1 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -1475,9 +1475,20 @@ consensus sequences.") (add-before 'build 'build-libssw (lambda _ (with-directory-excursion "libs/striped_smith_waterman" - (invoke "make" "libssw.so"))))))) - (inputs - `(("python-biopython" ,python-biopython) + (invoke "make" "libssw.so")))) + (add-before 'build 'fix-reference-to-ccs + (lambda* (#:key inputs #:allow-other-keys) + (substitute* "CIRI_long/pipeline.py" + (("'ccs -i") + (string-append "'" + (assoc-ref inputs "circtools") "/bin/ccs" + " -i"))) + ;; yuck! + (substitute* "CIRI_long/main.py" + (("os.chmod\\(lib_path.*") ""))))))) + (inputs + `(("circtools" ,circtools) + ("python-biopython" ,python-biopython) ("python-bwapy" ,python-bwapy) ("python-cython" ,python-cython) ("python-levenshtein" ,python-levenshtein) -- cgit v1.2.3