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| author | Ricardo Wurmus <rekado@elephly.net> | 2021-11-11 14:44:37 +0000 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2021-11-11 15:39:19 +0000 |
| commit | c4e5fabb6ef1a07967960f9b585847503cca0613 (patch) | |
| tree | a3b9f114ecb96cc23e37053ab63e6d4409f69ae2 | |
| parent | 6be47c5bc56b4a2d3183a58d1c9fb2e0846c7f0f (diff) | |
| download | guix-patches-c4e5fabb6ef1a07967960f9b585847503cca0613.tar guix-patches-c4e5fabb6ef1a07967960f9b585847503cca0613.tar.gz | |
gnu: ciri-long: Fix reference to ccs.
* gnu/packages/bioinformatics.scm (ciri-long)[arguments]: Add build phase
"fix-reference-to-ccs".
[inputs]: Add circtools.
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 17 |
1 files 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) |