01/01: gnu: bwa-meth: Capture one more reference to "bwa".

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit 79c6d8781b1e3d09e1e1555675c144d821487535
Author: Ricardo Wurmus <address@hidden>
Date:   Thu Sep 5 12:03:38 2019 +0200

    gnu: bwa-meth: Capture one more reference to "bwa".
    
    Reported by: Alexander.Blume <address@hidden>
    
    * gnu/packages/bioinformatics.scm (bwa-meth)[arguments]: Capture invocation 
of
    "bwa index" to retain reference to "bwa" package.
---
 gnu/packages/bioinformatics.scm | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index f590170..f976cad 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)))))