[med-svn] r11906 - trunk/packages/trimmomatic/trunk/debian
Andreas Tille
tille at alioth.debian.org
Thu Jul 26 17:22:22 UTC 2012
Author: tille
Date: 2012-07-26 17:22:22 +0000 (Thu, 26 Jul 2012)
New Revision: 11906
Added:
trunk/packages/trimmomatic/trunk/debian/TrimmomaticPE.1
trunk/packages/trimmomatic/trunk/debian/manifest
trunk/packages/trimmomatic/trunk/debian/manpages
Modified:
trunk/packages/trimmomatic/trunk/debian/changelog
trunk/packages/trimmomatic/trunk/debian/rules
trunk/packages/trimmomatic/trunk/debian/trimmomatic.links
Log:
Mass commit which makes the package ready for upload (IMHO)
Added: trunk/packages/trimmomatic/trunk/debian/TrimmomaticPE.1
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/TrimmomaticPE.1 (rev 0)
+++ trunk/packages/trimmomatic/trunk/debian/TrimmomaticPE.1 2012-07-26 17:22:22 UTC (rev 11906)
@@ -0,0 +1,104 @@
+.TH "TRIMMOMATICPE" "1" "July 2012" "Trimmomatic 0.22" "Trimmomatic Manual"
+.SH "NAME"
+TrimmomaticPE \- flexible read trimming tool for Illumina NGS data
+.SH "SYNOPSIS"
+Paired End Mode:
+.P
+\fBTrimmomaticPE\fR [\-threads \fIthreads\fR] [\-phred33 | \-phred64] [\-trimlog \fIlogFile\fR] \fIpaired output 1\fR \fIunpaired output 1\fR \fIpaired output 2\fR \fIunpaired output 2\fR \fIstep 1\fR \.\.\.
+.P
+Single End Mode:
+.P
+\fBTrimmomaticSE\fR [\-threads \fIthreads\fR] [\-phred33 | \-phred64] [\-trimlog \fIlogFile\fR] \fIoutput\fR \fIstep 1\fR \.\.\.
+
+.SH "DESCRIPTION"
+Trimmomatic performs a variety of useful trimming tasks for illumina
+paired-end and single ended data.The selection of trimming steps and
+their associated parameters are supplied on the command line.
+
+.SH "OPTIONS"
+.PP
+\fB\-phred\fR
+.RS 4
+If no quality score is specified, phred\-64 is the default.
+.RE
+.PP
+\fB\-trimlog\fR
+.RS 4
+Specifying a trimlog file creates a log of all read trimmings, indicating the following details:
+.IP "\(bu" 4
+the read name
+.IP "\(bu" 4
+the surviving sequence length
+.IP "\(bu" 4
+the location of the first surviving base, aka\. the amount trimmed from the start
+.IP "\(bu" 4
+the location of the last surviving base in the original read
+.IP "\(bu" 4
+the amount trimmed from the end
+.IP "" 0
+Multiple steps can be specified as required, by using additional arguments at the end\.
+.
+.P
+Most steps take one or more settings, delimited by \':\' (a colon)
+.
+.P
+Step options:
+.
+.IP "" 4
+.
+.nf
+ILLUMINACLIP:<fastaWithAdaptersEtc>:<seed mismatches>:<palindrome clip threshold>:<simple clip threshold>
+ fastaWithAdaptersEtc: specifies the path to a fasta file containing all the adapters, PCR sequences etc\.
+ The naming of the various sequences within this file determines how they are used\. See below\.
+ 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\.
+
+SLIDINGWINDOW:<windowSize>:<requiredQuality>
+ windowSize: specifies the number of bases to average across
+ requiredQuality: specifies the average quality required\.
+
+LEADING:<quality>
+ quality: Specifies the minimum quality required to keep a base\.
+
+TRAILING:<quality>
+ quality: Specifies the minimum quality required to keep a base\.
+
+CROP:<length>
+ length: The number of bases to keep, from the start of the read\.
+
+HEADCROP:<length>
+ length: The number of bases to remove from the start of the read\.
+
+MINLENGTH:<length>
+ length: Specifies the minimum length of reads to be kept\.
+.fi
+.
+.IP "" 0
+.
+.P
+Trimming Order
+.P
+Trimming occurs in the order which the steps are specified on the command line\. It is recommended in most cases that adapter clipping, if required, is done as early as possible\.
+.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
+.
+.P
+This will perform the following:
+.IP "" 4
+.nf
+Remove adapters
+Remove leading low quality or N bases (below quality 3)
+Remove trailing low quality or N bases (below quality 3)
+Scan the read with a 4\-base wide sliding window, cutting when the average quality per base drops below 15
+Drop reads below the 36 bases long
+.fi
+.
+.IP "" 0
+.
+.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
Modified: trunk/packages/trimmomatic/trunk/debian/changelog
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/changelog 2012-07-26 16:57:37 UTC (rev 11905)
+++ trunk/packages/trimmomatic/trunk/debian/changelog 2012-07-26 17:22:22 UTC (rev 11906)
@@ -1,13 +1,6 @@
trimmomatic (0.22-1) UNRELEASED; urgency=low
- * New upstream version, initial release (Closes: #682213).
- * Added dependency on libjblip2-java
- * Added symbolic link from trimmomatic.jar to trimmomatic-0.22.jar
+ * Initial release (Closes: #682213).
- -- Steffen Moeller <moeller at debian.org> Fri, 20 Jul 2012 11:15:20 +0200
+ -- Andreas Tille <tille at debian.org> Wed, 25 Jul 2012 16:34:43 +0200
-trimmomatic (0.17-1) UNRELEASED; urgency=low
-
- * Initial packaging.
-
- -- Andreas Tille <tille at debian.org> Fri, 18 Nov 2011 19:12:40 +0100
Added: trunk/packages/trimmomatic/trunk/debian/manifest
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/manifest (rev 0)
+++ trunk/packages/trimmomatic/trunk/debian/manifest 2012-07-26 17:22:22 UTC (rev 11906)
@@ -0,0 +1,2 @@
+/usr/share/java/trimmomatic.jar:
+ Class-Path: /usr/share/java/jbzip2.jar
Added: trunk/packages/trimmomatic/trunk/debian/manpages
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/manpages (rev 0)
+++ trunk/packages/trimmomatic/trunk/debian/manpages 2012-07-26 17:22:22 UTC (rev 11906)
@@ -0,0 +1 @@
+debian/*.1
Modified: trunk/packages/trimmomatic/trunk/debian/rules
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/rules 2012-07-26 16:57:37 UTC (rev 11905)
+++ trunk/packages/trimmomatic/trunk/debian/rules 2012-07-26 17:22:22 UTC (rev 11906)
@@ -4,6 +4,9 @@
# Andreas Tille <tille at debian.org>
# GPL
+pkg := $(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
+ver := $(shell dpkg-parsechangelog | awk '/^Version/ { print $$2 }' | cut -d- -f1 )
+
%:
dh $@ --with javahelper
@@ -13,6 +16,11 @@
touch dist/unpack/AUTHORS
ant
+override_dh_link:
+ dh_link
+ # enable symlinking without any need to edit for new versions
+ dh_link usr/share/java/$(pkg)-$(ver).jar usr/share/java/$(pkg).jar
+
get-orig-source:
# uscan --verbose --force-download --repack --rename
. debian/get-orig-source
Modified: trunk/packages/trimmomatic/trunk/debian/trimmomatic.links
===================================================================
--- trunk/packages/trimmomatic/trunk/debian/trimmomatic.links 2012-07-26 16:57:37 UTC (rev 11905)
+++ trunk/packages/trimmomatic/trunk/debian/trimmomatic.links 2012-07-26 17:22:22 UTC (rev 11906)
@@ -1,2 +1,2 @@
-usr/share/java/trimmomatic-0.22.jar usr/share/java/trimmomatic.jar
-usr/bin/TrimmomaticPE usr/bin/TrimmomaticSE
+usr/bin/TrimmomaticPE usr/bin/TrimmomaticSE
+usr/share/man/man1/TrimmomaticPE.1.gz usr/share/man/man1/TrimmomaticSE.1.gz
\ No newline at end of file
More information about the debian-med-commit
mailing list