[med-svn] [metabit] 01/03: In Debian the picard tools Jar is named picard.jar

[Andreas Tille]

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tille pushed a commit to branch master
in repository metabit.

commit 9e4f0fedeb100dd3806608ee265806232638fad8
Author: Andreas Tille <tille at debian.org>
Date:   Tue Jul 26 14:55:29 2016 +0200

    In Debian the picard tools Jar is named picard.jar
---
 debian/control                                    |  3 ++-
 debian/patches/debian_packaged_picard_tools.patch | 17 +++++++++++++++++
 debian/patches/series                             |  1 +
 3 files changed, 20 insertions(+), 1 deletion(-)

diff --git a/debian/control b/debian/control
index 170765e..1b350a5 100644
--- a/debian/control
+++ b/debian/control
@@ -20,7 +20,8 @@ Depends: ${python:Depends},
          bowtie2,
          r-base-core,
          metaphlan2,
-         python-pysam
+         python-pysam,
+         libpicard-java
 Description: analysing microbial profiles from high-throughput sequencing shotgun data
  MetaBIT is an integrative and automated metagenomic pipeline for
  analysing microbial profiles from high-throughput sequencing
diff --git a/debian/patches/debian_packaged_picard_tools.patch b/debian/patches/debian_packaged_picard_tools.patch
new file mode 100644
index 0000000..f208461
--- /dev/null
+++ b/debian/patches/debian_packaged_picard_tools.patch
@@ -0,0 +1,17 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Updates: Mon, 25 Jul 2016 14:09:29 +0200
+Description: In Debian the picard tools Jar is named picard.jar
+
+--- a/nodes/picard_simple.py
++++ b/nodes/picard_simple.py
+@@ -81,6 +81,10 @@ class MarkDuplicatesNode(PicardNode):
+     def customize(cls, config, input_bams, output_bam, output_metrics=None,
+                   keep_dupes=False, dependencies=()):
+         jar_file = os.path.join(config.jar_root, "MarkDuplicates.jar")
++        if not os.path.exists(jar_file):
++            jar_file = os.path.join(config.jar_root, "picard.jar")
++        if not os.path.exists(jar_file):
++            raise "JAR file %s not found.  Please install picard." % jar_file
+         params = AtomicJavaCmdBuilder(jar_file, jre_options=config.jre_options)
+ 
+         input_bam = safe_coerce_to_tuple(input_bams)[0]
diff --git a/debian/patches/series b/debian/patches/series
index d44c6a5..fdd23d8 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,3 +1,4 @@
 use_debian_packaged_yaml.patch
 safely_detect_metaphlan.patch
 jar_root.patch
+debian_packaged_picard_tools.patch

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