06/06: gnu: pigx-rnaseq: Adjust to upgrade of salmon.

[guix-commits]

rekado pushed a commit to branch master
in repository guix.

commit be067c908c90b9d9f798fdf36f744f72c884f3bd
Author: Ricardo Wurmus <rekado@elephly.net>
AuthorDate: Mon Jun 7 16:49:12 2021 +0200

    gnu: pigx-rnaseq: Adjust to upgrade of salmon.
    
    * gnu/packages/bioinformatics.scm (pigx-rnaseq)[arguments]: Add phase
    "use-latest-salmon".
---
 gnu/packages/bioinformatics.scm | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index a34b123..206c193 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -10371,6 +10371,13 @@ once.  This package provides tools to perform Drop-seq 
analyses.")
      `(#:parallel-tests? #f             ; not supported
        #:phases
        (modify-phases %standard-phases
+         ;; See https://github.com/BIMSBbioinfo/pigx_rnaseq/issues/96
+         (add-after 'unpack 'use-latest-salmon
+           (lambda _
+             (substitute* "snakefile.py"
+               (("\"sa.bin\"") "\"pos.bin\""))
+             (substitute* "tests/test_salmon/test_salmon_index.sh.in"
+               (("sa.bin") "pos.bin"))))
          ;; "test.sh" runs STAR, which requires excessive amounts of memory.
          (add-after 'unpack 'disable-resource-intensive-test
            (lambda _