[med-svn] r18870 - trunk/packages/trimmomatic/trunk/debian

[Andreas Tille]

Author: tille
Date: 2015-02-27 12:29:52 +0000 (Fri, 27 Feb 2015)
New Revision: 18870

Modified:
   trunk/packages/trimmomatic/trunk/debian/TrimmomaticPE.1
   trunk/packages/trimmomatic/trunk/debian/changelog
Log:
Also adjust manpage to make sure users will be properly informed about the adapter location since the package might be useless without this information


Modified: trunk/packages/trimmomatic/trunk/debian/TrimmomaticPE.1
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/TrimmomaticPE.1	2015-02-26 22:43:47 UTC (rev 18869)
+++ trunk/packages/trimmomatic/trunk/debian/TrimmomaticPE.1	2015-02-27 12:29:52 UTC (rev 18870)
@@ -53,6 +53,8 @@
     seedMismatches: specifies the maximum mismatch count which will still allow a full match to be performed
     palindromeClipThreshold: specifies how accurate the match between the two \'adapter ligated\' reads must be for PE palindrome read alignment\.
     simpleClipThreshold: specifies how accurate the match between any adapter etc\. sequence must be against a read\.
+    \.
+    The adapters are installed on the Debian system at /usr/share/trimmomatic/\.
 
 SLIDINGWINDOW:<windowSize>:<requiredQuality>
     windowSize: specifies the number of bases to average across
@@ -83,7 +85,7 @@
 .SH "EXAMPLES"
 Paired End:
 .P
-\fBTrimmomaticPE\fR s_1_1_sequence\.txt\.gz s_1_2_sequence\.txt\.gz lane1_forward_paired\.fq\.gz lane1_forward_unpaired\.fq\.gz lane1_reverse_paired\.fq\.gz lane1_reverse_unpaired\.fq\.gz ILLUMINACLIP:illuminaClipping\.fa:2:40:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
+\fBTrimmomaticPE\fR s_1_1_sequence\.txt\.gz s_1_2_sequence\.txt\.gz lane1_forward_paired\.fq\.gz lane1_forward_unpaired\.fq\.gz lane1_reverse_paired\.fq\.gz lane1_reverse_unpaired\.fq\.gz ILLUMINACLIP:/usr/share/trimmomatic/illuminaClipping\.fa:2:40:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
 .
 .P
 This will perform the following:
@@ -101,4 +103,4 @@
 .P
 The equivalent for single\-ended reads is:
 .P
-\fBTrimmomaticSE\fR s_1_1_sequence\.txt\.gz lane1_forward\.fq\.gz ILLUMINACLIP:illuminaClipping\.fa:2:40:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
+\fBTrimmomaticSE\fR s_1_1_sequence\.txt\.gz lane1_forward\.fq\.gz ILLUMINACLIP:/usr/share/trimmomatic/illuminaClipping\.fa:2:40:15 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36

Modified: trunk/packages/trimmomatic/trunk/debian/changelog
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/changelog	2015-02-26 22:43:47 UTC (rev 18869)
+++ trunk/packages/trimmomatic/trunk/debian/changelog	2015-02-27 12:29:52 UTC (rev 18870)
@@ -1,3 +1,12 @@
+trimmomatic (0.32+dfsg-4) unstable; urgency=medium
+
+  * Also adjust manpage to make sure users will be properly informed
+    about the adapter location since the package might be useless
+    without this information (so the issue is closely related to
+    bug #779296)
+
+ -- Andreas Tille <tille at debian.org>  Fri, 27 Feb 2015 12:28:04 +0100
+
 trimmomatic (0.32+dfsg-3) unstable; urgency=medium
 
   * Install adapter files and document their usage in d/README.Debian