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gnu: ciri-long: Fix reference to ccs.

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* gnu/packages/bioinformatics.scm (ciri-long)[arguments]: Add build phase
"fix-reference-to-ccs".
[inputs]: Add circtools.
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Ricardo Wurmus 2021-11-11 14:44:37 +00:00
parent 6be47c5bc5
commit c4e5fabb6e
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1 changed files with 13 additions and 2 deletions
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gnu/packages/bioinformatics.scm
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@ -1475,9 +1475,20 @@ (define-public ciri-long
(add-before 'build 'build-libssw (add-before 'build 'build-libssw
(lambda _ (lambda _
(with-directory-excursion "libs/striped_smith_waterman" (with-directory-excursion "libs/striped_smith_waterman"
(invoke "make" "libssw.so"))))))) (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 (inputs
`(("python-biopython" ,python-biopython) `(("circtools" ,circtools)
("python-biopython" ,python-biopython)
("python-bwapy" ,python-bwapy) ("python-bwapy" ,python-bwapy)
("python-cython" ,python-cython) ("python-cython" ,python-cython)
("python-levenshtein" ,python-levenshtein) ("python-levenshtein" ,python-levenshtein)