[med-svn] [metabit] 01/01: Fix picard-tools call

[Andreas Tille]

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tille pushed a commit to branch master
in repository metabit.

commit 67fbd187139f2f189e7386f793e3a119a617b1fc
Author: Andreas Tille <tille at debian.org>
Date:   Thu Aug 4 11:02:26 2016 +0200

    Fix picard-tools call
---
 .../patches/debian_picard_tools_version_check.patch | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/debian/patches/debian_picard_tools_version_check.patch b/debian/patches/debian_picard_tools_version_check.patch
index dc88e5c..40dcda5 100644
--- a/debian/patches/debian_picard_tools_version_check.patch
+++ b/debian/patches/debian_picard_tools_version_check.patch
@@ -1,14 +1,17 @@
 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
+ The picard-tools call is fixed in general since it always needs a module
+ name which is appended here in the hope, that only MarkDuplicates is used.
 
---- 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")
+--- a/pypeline/atomiccmd/builder.py
++++ b/pypeline/atomiccmd/builder.py
+@@ -364,7 +364,7 @@ class AtomicJavaCmdBuilder(AtomicCmdBuil
+                 call.append("-Xmx4g")
  
-         name = "Picard " + os.path.basename(jar_file)
+         version = self._get_java_version(java_version)
+-        call.extend(("-jar", "%(AUX_JAR)s"))
++        call.extend(("-jar", "%(AUX_JAR)s", "MarkDuplicates"))
+         AtomicCmdBuilder.__init__(self, call,
+                                   AUX_JAR=jar,
+                                   CHECK_JRE=version,

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