67/69: gnu: ciri-long: Fix reference to ccs.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit c4e5fabb6ef1a07967960f9b585847503cca0613
Author: Ricardo Wurmus <rek...@elephly.net>
AuthorDate: Thu Nov 11 14:44:37 2021 +0000

    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 13bd7b5..3455029 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)