[med-svn] [mapping-pipeline] 10/10: COnfig in /etc

[Andreas Tille]

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tille pushed a commit to branch master
in repository mapping-pipeline.

commit 124837ebe731976a79e8a88e36a721dc4bd12894
Author: Andreas Tille <tille at debian.org>
Date:   Tue Feb 21 13:52:19 2017 +0100

    COnfig in /etc
---
 debian/patches/config.patch | 36 ++++++++++++++++++++++++++++++++++++
 1 file changed, 36 insertions(+)

diff --git a/debian/patches/config.patch b/debian/patches/config.patch
new file mode 100644
index 0000000..c995bc7
--- /dev/null
+++ b/debian/patches/config.patch
@@ -0,0 +1,36 @@
+Author: Andreas Tille
+Last-Update: Di 21. Feb 13:36:52 CET 2017
+Description: Config goes to /etc and uses default Debian tools
+
+--- a/mapping.py
++++ b/mapping.py
+@@ -444,7 +444,7 @@ class MAPPING:
+             # Turn off help, so we print all options in response to -h
+             add_help=False
+         )
+-        config = os.path.join(os.path.dirname(__file__), 'run.config')
++        config = os.path.join('/etc/mapping-pipeline', 'run.config')
+         if '--config' not in sys.argv and os.path.isfile(config):
+             sys.argv += ['--config', config]
+         conf_parser.add_argument("--config", help="Specify config file", metavar="FILE")
+@@ -482,7 +482,7 @@ class MAPPING:
+         self.optional.add_argument('--bwa', dest='bwa', nargs='?', default='/usr/bin', type=self._valid_bwa, help='Path to folder containg bwa.')
+         self.optional.add_argument('--bowtie2', dest='bowtie2', nargs='?', default='/usr/bin/', type=self._valid_bowtie2, help='Path to folder containing bowtie2.')
+         self.optional.add_argument('--picard', dest='picard', nargs='?', default='/usr/bin/', type=str, help='Path to folder containing picard.jar')
+-        self.optional.add_argument('--config', help='Define config file to read parameters from. If run.config exists in the source directory, it is if --config is not defined.')
++        self.optional.add_argument('--config', help='Define config file to read parameters from. Default is /etc/mapping-pipeline/run.config .')
+         self.args = self.parser.parse_args(remaining_argv)
+         if self.args.join_sample and self.args.join:
+             raise argparse.ArgumentTypeError('Only either --join or --join_sample are allowed')
+--- a/run.config
++++ b/run.config
+@@ -1,5 +1,5 @@
+---samtools=/opt/common/pipelines/tools/samtools-1.3.1/
+---bwa=/opt/common/pipelines/tools/bwa-0.7.15/
++--samtools=/usr/bin/
++--bwa=/usr/bin/
+ --bowtie2=/usr/bin/
+---picard=/opt/common/pipelines/tools/picard-2.7.1/
+---java=java-1.8
++--picard=/usr/share/java/
++--java=java

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