>From d1c70ba0a701a31469dcae2b1a0efb624e5409d1 Mon Sep 17 00:00:00 2001
From: Ben Woodcroft <address@hidden>
Date: Fri, 23 Dec 2016 22:13:33 +1000
Subject: [PATCH] gnu: multiqc: Update to 0.9.

* gnu/packages/bioinformatics.scm (multiqc): Update to 0.9.
[origin]: Add patch.
[arguments]: Run tests.
[native-inputs]: Add python-nose, multiqc-test-data.
* gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
---
 gnu/local.mk                                       |  1 +
 gnu/packages/bioinformatics.scm                    | 28 ++++++++++++++++++++--
 .../patches/multiqc-fix-git-subprocess-error.patch | 15 ++++++++++++
 3 files changed, 42 insertions(+), 2 deletions(-)
 create mode 100644 gnu/packages/patches/multiqc-fix-git-subprocess-error.patch

diff --git a/gnu/local.mk b/gnu/local.mk
index ee8f1e591..bde8bc235 100644
--- a/gnu/local.mk
+++ b/gnu/local.mk
@@ -727,6 +727,7 @@ 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	\
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 912941e11..0cbbce1fc 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -7853,15 +7853,39 @@ 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
+     `(#:phases
+       (modify-phases %standard-phases
+         (replace 'check
+           (lambda* (#:key inputs #:allow-other-keys)
+             (let ((data (assoc-ref inputs "multiqc-test-data")))
+               (setenv "PYTHONPATH"
+                       (string-append (getcwd) ":" (getenv "PYTHONPATH")))
+               (with-directory-excursion data
+                 (zero? (system* "python3" "-munittest" "discover")))))))))
+    (native-inputs
+     `(("python-nose" ,python-nose)
+       ("multiqc-test-data"
+        ,(let ((commit "32bf18b4d7c46496ae50bfaf4c94a9df3afd0491"))
+           (origin
+             (method git-fetch)
+             (uri (git-reference
+                   (url "https://github.com/ewels/MultiQC_TestData.git")
+                   (commit commit)))
+             (file-name (string-append "multiqc-test-data" commit "-checkout"))
+             (sha256
+              (base32
+               "079pcr6j2nk0v238qwsslgk480rv82xwsjyy4lf6v48l6zj4llm0")))))))
     (propagated-inputs
      `(("python-jinja2" ,python-jinja2)
        ("python-simplejson" ,python-simplejson)
diff --git a/gnu/packages/patches/multiqc-fix-git-subprocess-error.patch b/gnu/packages/patches/multiqc-fix-git-subprocess-error.patch
new file mode 100644
index 000000000..50807e2b7
--- /dev/null
+++ b/gnu/packages/patches/multiqc-fix-git-subprocess-error.patch
@@ -0,0 +1,15 @@
+Without this patch, the incorrect exception is caught when 'git' is not in PATH.
+
+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)
+ 
-- 
2.11.0