[med-svn] [trimmomatic] 02/03: Trimmomatic shall find adapters by name

[Steffen Möller]

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moeller pushed a commit to branch master
in repository trimmomatic.

commit 4b8a42f9918e2da233e32319f0c08f7fadd71c24
Author: Steffen Moeller <moeller at debian.org>
Date:   Wed Mar 2 14:16:37 2016 +0100

    Trimmomatic shall find adapters by name
---
 debian/README.source                               | 13 ++++++++++++
 debian/changelog                                   |  1 +
 .../patches/search_in_usr_share_trimmomatic.patch  | 24 ++++++++++++++++++++++
 debian/patches/series                              |  1 +
 4 files changed, 39 insertions(+)

diff --git a/debian/README.source b/debian/README.source
new file mode 100644
index 0000000..e295730
--- /dev/null
+++ b/debian/README.source
@@ -0,0 +1,13 @@
+Trimmomatic
+===========
+
+The following patches are applied to Trimmomatic:
+
+buildxmlJbzip2.patch:
+	Learn about /usr/share/java.
+
+remove_jar_version.path:
+	We do only produce a trimmomatic.jar, nothing versioned.
+
+search_in_usr_share_trimmomatic.patch
+	Also search for adapter sequences in /usr/share/trimmomatic
diff --git a/debian/changelog b/debian/changelog
index 9eb6bf4..beaf1e6 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,6 +2,7 @@ trimmomatic (0.35+dfsg-2) UNRELEASED; urgency=medium
 
   * Introduced EDAM ontology information to 
     debian/upstream/edam
+  * Added patch to find adapters in /usr/share/trimmomatic [still needs to be tested, don't upload]
 
  -- Steffen Moeller <moeller at debian.org>  Fri, 05 Feb 2016 15:38:41 +0100
 
diff --git a/debian/patches/search_in_usr_share_trimmomatic.patch b/debian/patches/search_in_usr_share_trimmomatic.patch
new file mode 100644
index 0000000..272ad80
--- /dev/null
+++ b/debian/patches/search_in_usr_share_trimmomatic.patch
@@ -0,0 +1,24 @@
+Index: trimmomatic/src/org/usadellab/trimmomatic/trim/IlluminaClippingTrimmer.java
+===================================================================
+--- trimmomatic.orig/src/org/usadellab/trimmomatic/trim/IlluminaClippingTrimmer.java
++++ trimmomatic/src/org/usadellab/trimmomatic/trim/IlluminaClippingTrimmer.java
+@@ -49,7 +49,18 @@ public class IlluminaClippingTrimmer imp
+ 	{
+ 		String arg[] = args.split(":");
+ 		
+-		File seqs=new File(arg[0]);
++		File seqs;
++		if (File.exists(arg[0])) {
++			seqs = new File(arg[0]);
++		}
++		else if (!arg[0].startsWith("/") and !arg[0].startsWith("..") and File.exists("/usr/share/trimmomatic/"+arg[0])) {
++			seqs = new File("/usr/share/trimmomatic/"+arg[0]);
++		}
++		else {
++			System.err.println("E: Could not find '"+arg[0]+"' in local directory or /usr/share/trimmomatic.")
++			System.exit(1);
++		}
++
+ 
+ 		int seedMaxMiss = Integer.parseInt(arg[1]);
+ 		int minPalindromeLikelihood = Integer.parseInt(arg[2]);
diff --git a/debian/patches/series b/debian/patches/series
index 59b36fe..cf3278f 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 buildxmlJbzip2.patch
 remove_jar_version.path
+search_in_usr_share_trimmomatic.patch

-- 
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