summary refs log tree commit diff
path: root/gnu/packages/bioinformatics.scm
diff options
context:
space:
mode:
authorRicardo Wurmus <rekado@elephly.net>2019-09-05 12:03:38 +0200
committerRicardo Wurmus <rekado@elephly.net>2019-09-05 12:06:43 +0200
commit79c6d8781b1e3d09e1e1555675c144d821487535 (patch)
tree6e5d06ecba82c80f3b1b735fc4a94d22c8b41923 /gnu/packages/bioinformatics.scm
parent0e8b91dbc45306984d682307d8b40b0e323bb4be (diff)
downloadguix-79c6d8781b1e3d09e1e1555675c144d821487535.tar.gz
gnu: bwa-meth: Capture one more reference to "bwa".
Reported by: Alexander.Blume <Alexander.Blume@mdc-berlin.de>

* gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Capture invocation of
"bwa index" to retain reference to "bwa" package.
Diffstat (limited to 'gnu/packages/bioinformatics.scm')
-rw-r--r--gnu/packages/bioinformatics.scm4
1 files changed, 2 insertions, 2 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f5901703ce..f976cad22f 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1767,8 +1767,8 @@ well as many of the command line options.")
          (add-after 'unpack 'keep-references-to-bwa
            (lambda* (#:key inputs #:allow-other-keys)
              (substitute* "bwameth.py"
-               (("bwa mem")
-                (string-append (which "bwa") " mem"))
+               (("bwa (mem|index)" _ command)
+                (string-append (which "bwa") " " command))
                ;; There's an ill-advised check for "samtools" on PATH.
                (("^checkX.*") ""))
              #t)))))