[med-svn] [metabit] 02/02: Fix version check

[Andreas Tille]

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tille pushed a commit to branch master
in repository metabit.

commit 518eb76ec826e3157bd4651ce6f16ec8af26019f
Author: Andreas Tille <tille at debian.org>
Date:   Fri Jul 29 10:50:09 2016 +0200

    Fix version check
---
 debian/patches/debian_picard_tools_version_check.patch | 14 ++++++++++++++
 debian/patches/series                                  |  1 +
 2 files changed, 15 insertions(+)

diff --git a/debian/patches/debian_picard_tools_version_check.patch b/debian/patches/debian_picard_tools_version_check.patch
new file mode 100644
index 0000000..dc88e5c
--- /dev/null
+++ b/debian/patches/debian_picard_tools_version_check.patch
@@ -0,0 +1,14 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Updates: Mon, 25 Jul 2016 14:09:29 +0200
+Description: Version checks for picard tools need to specify a module name
+
+--- a/nodes/picard_simple.py
++++ b/nodes/picard_simple.py
+@@ -47,6 +47,7 @@ def _picard_version(config, jar_file):
+         params = AtomicJavaCmdBuilder(jar_file,
+                                       temp_root=config.temp_root,
+                                       jre_options=config.jre_options)
++        params.add_value("MarkDuplicates")
+         params.add_value("--version")
+ 
+         name = "Picard " + os.path.basename(jar_file)
diff --git a/debian/patches/series b/debian/patches/series
index dba726e..675e52f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -3,3 +3,4 @@ safely_detect_metaphlan.patch
 jar_root.patch
 debian_packaged_picard_tools.patch
 debian_packaged_lefse.patch
+debian_picard_tools_version_check.patch

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