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commit 67fbd187139f2f189e7386f793e3a119a617b1fc Author: Andreas Tille <[email protected]> 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 <[email protected]> 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, -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/metabit.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
