[med-svn] [metabit] 02/02: Set jar_root to /usr/share/java

[Andreas Tille]

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tille pushed a commit to branch master
in repository metabit.

commit 5ca4512d6cfe4626a3c800a84c7cf1ad9205902e
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jul 26 14:31:38 2016 +0200

    Set jar_root to /usr/share/java
---
 debian/patches/jar_root.patch | 26 ++++++++++++++++++++++++++
 debian/patches/series         |  1 +
 2 files changed, 27 insertions(+)

diff --git a/debian/patches/jar_root.patch b/debian/patches/jar_root.patch
new file mode 100644
index 0000000..51ea946
--- /dev/null
+++ b/debian/patches/jar_root.patch
@@ -0,0 +1,26 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Updates: Mon, 25 Jul 2016 14:09:29 +0200
+Description: set jar_root to /usr/share/java
+
+--- a/pypeline/tools/bam_pipeline/config.py
++++ b/pypeline/tools/bam_pipeline/config.py
+@@ -64,7 +64,7 @@ def _run_config_parser(argv):
+     parser.add_option_group(group)
+ 
+     group  = optparse.OptionGroup(parser, "Required paths")
+-    group.add_option("--jar-root", default = PerHostValue("~/install/jar_root", is_path = True),
++    group.add_option("--jar-root", default = PerHostValue("/usr/share/java", is_path = True),
+                      help = "Folder containing Picard JARs (http://picard.sf.net), " \
+                             "and GATK (www.broadinstitute.org/gatk). " \
+                             "The latter is only required if realigning is enabled. " \
+--- a/config.py
++++ b/config.py
+@@ -84,7 +84,7 @@ def _run_config_parser(argv):
+     parser.add_option_group(group)
+ 
+     group  = optparse.OptionGroup(parser, "Required paths")
+-    group.add_option("--jar-root", default = PerHostValue("~/install/jar_root",
++    group.add_option("--jar-root", default = PerHostValue("/usr/share/java",
+                                                           is_path = True),
+                      help = "Folder containing Picard JARs (http://picard.sf.net) " \
+                      "[%default]")
diff --git a/debian/patches/series b/debian/patches/series
index 2c3639f..d44c6a5 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 use_debian_packaged_yaml.patch
 safely_detect_metaphlan.patch
+jar_root.patch

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