3 files changed, 24 insertions(+), 2 deletions(-)

M gnu/local.mk
M gnu/packages/bioinformatics.scm
A gnu/packages/patches/multiqc-fix-git-subprocess-error.patch

@@ 730,6 730,7 @@ dist_patch_DATA =						\
   %D%/packages/patches/mpc123-initialize-ao.patch		\
   %D%/packages/patches/mplayer2-theora-fix.patch		\
   %D%/packages/patches/module-init-tools-moduledir.patch	\
+  %D%/packages/patches/multiqc-fix-git-subprocess-error.patch	\
   %D%/packages/patches/mumps-build-parallelism.patch		\
   %D%/packages/patches/mupdf-build-with-openjpeg-2.1.patch	\
   %D%/packages/patches/mupen64plus-ui-console-notice.patch	\

@@ 7855,15 7855,20 @@ replacement for strverscmp.")
 (define-public multiqc
   (package
     (name "multiqc")
-    (version "0.6")
+    (version "0.9")
     (source
      (origin
        (method url-fetch)
        (uri (pypi-uri "multiqc" version))
        (sha256
         (base32
-         "0avw11h63ldpxy5pizc3wl1wa01ha7q10wb240nggsjz3jaqvyiy"))))
+         "12gs1jw2jrxrij529rnl5kaqxfcqn15yzcsggxkfhdx634ml0cny"))
+       (patches (search-patches "multiqc-fix-git-subprocess-error.patch"))))
     (build-system python-build-system)
+    (arguments
+     ;; Tests are to be introduced in the next version, see
+     ;; https://github.com/ewels/MultiQC/issues/376
+     `(#:tests? #f))
     (propagated-inputs
      `(("python-jinja2" ,python-jinja2)
        ("python-simplejson" ,python-simplejson)

@@ 0,0 1,16 @@
+Without this patch, the incorrect exception is caught when 'git' is not in
+PATH.  See https://github.com/ewels/MultiQC/pull/377.
+
+diff --git a/multiqc/utils/config.py b/multiqc/utils/config.py
+index 01fa554..4a11793 100755
+--- a/multiqc/utils/config.py
++++ b/multiqc/utils/config.py
+@@ -28,7 +28,7 @@ try:
+     git_hash = subprocess.check_output(['git', 'rev-parse', 'HEAD'], stderr=subprocess.STDOUT)
+     git_hash_short = git_hash[:7]
+     version = '{} ({})'.format(version, git_hash_short)
+-except subprocess.CalledProcessError:
++except (subprocess.CalledProcessError, FileNotFoundError):
+     pass
+ os.chdir(cwd)
+