Bug#779342: unblock: trimmomatic/0.32+dfsg-4
Package: release.debian.org
Severity: normal
User: release.debian.org@packages.debian.org
Usertags: unblock
Please unblock package trimmomatic
A serious bug in trimmomatic (#779296) was detected by a user which
rendered the package useless for the intended application since some
important files were missing. Since upstream had a very weak user
interface it also had to made sure that the users will find the files.
Thus another upload after the actual bug fixing upload was done to
explain the important piece of information in the according manpage.
A debdiff is attached.
unblock trimmomatic/0.32+dfsg-4
-- System Information:
Debian Release: 7.8
APT prefers stable
APT policy: (500, 'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 3.2.0-4-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
diff -Nru trimmomatic-0.32+dfsg/debian/changelog trimmomatic-0.32+dfsg/debian/changelog
--- trimmomatic-0.32+dfsg/debian/changelog 2014-12-16 16:00:16.000000000 +0100
+++ trimmomatic-0.32+dfsg/debian/changelog 2015-02-27 13:17:30.000000000 +0100
@@ -1,3 +1,19 @@
+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@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
+ Closes: #779296
+
+ -- Andreas Tille <tille@debian.org> Thu, 26 Feb 2015 21:52:47 +0100
+
trimmomatic (0.32+dfsg-2) unstable; urgency=medium
* Fix bashism in wrapper script
diff -Nru trimmomatic-0.32+dfsg/debian/install trimmomatic-0.32+dfsg/debian/install
--- trimmomatic-0.32+dfsg/debian/install 2013-09-12 10:57:53.000000000 +0200
+++ trimmomatic-0.32+dfsg/debian/install 2015-02-26 22:21:39.000000000 +0100
@@ -1 +1,2 @@
debian/bin/* usr/bin
+adapters/* usr/share/trimmomatic
diff -Nru trimmomatic-0.32+dfsg/debian/README.Debian trimmomatic-0.32+dfsg/debian/README.Debian
--- trimmomatic-0.32+dfsg/debian/README.Debian 1970-01-01 01:00:00.000000000 +0100
+++ trimmomatic-0.32+dfsg/debian/README.Debian 2015-02-26 23:41:37.000000000 +0100
@@ -0,0 +1,11 @@
+Trimmomatic for Debian
+======================
+
+The adapters are installed to /usr/share/trimmomatic/*.fa
+Here is an example command line:
+
+ TrimmomaticSE -phred33 input.fq.gz output.fq.gz \
+ ILLUMINACLIP:/usr/share/trimmomatic/TruSeq3-SE.fa:2:30:10 \
+ LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
+
+ -- Andreas Tille <tille@debian.org> Thu, 26 Feb 2015 21:52:47 +0100
diff -Nru trimmomatic-0.32+dfsg/debian/TrimmomaticPE.1 trimmomatic-0.32+dfsg/debian/TrimmomaticPE.1
--- trimmomatic-0.32+dfsg/debian/TrimmomaticPE.1 2013-09-12 10:57:53.000000000 +0200
+++ trimmomatic-0.32+dfsg/debian/TrimmomaticPE.1 2015-02-27 12:27:04.000000000 +0100
@@ -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
Reply to: