[med-svn] r2728 - trunk/packages/ssake/trunk/debian
tille at alioth.debian.org
tille at alioth.debian.org
Mon Nov 24 13:15:58 UTC 2008
Author: tille
Date: 2008-11-24 13:15:58 +0000 (Mon, 24 Nov 2008)
New Revision: 2728
Added:
trunk/packages/ssake/trunk/debian/ssake-examples.dirs
trunk/packages/ssake/trunk/debian/ssake.1
trunk/packages/ssake/trunk/debian/ssake.dirs
trunk/packages/ssake/trunk/debian/ssake.manpages
Modified:
trunk/packages/ssake/trunk/debian/control
trunk/packages/ssake/trunk/debian/copyright
trunk/packages/ssake/trunk/debian/rules
Log:
Several fixes for packaging
Modified: trunk/packages/ssake/trunk/debian/control
===================================================================
--- trunk/packages/ssake/trunk/debian/control 2008-11-24 12:33:30 UTC (rev 2727)
+++ trunk/packages/ssake/trunk/debian/control 2008-11-24 13:15:58 UTC (rev 2728)
@@ -12,29 +12,33 @@
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/ssake/trunk/
Package: ssake
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, ${perl:Depends}
Description: assembling millions of very short DNA sequences
- SSAKE is a genomics application for assembling millions of very short DNA sequences.
+ SSAKE is a genomics application for assembling millions of very short
+ DNA sequences.
.
- The Short Sequence Assembly by K-mer search and 3' read Extension (SSAKE) is a
- genomics application for aggressively assembling millions of short nucleotide
- sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix
- tree. SSAKE is designed to help leverage the information from short sequences reads
- by stringently clustering them into contigs that can be used to characterize novel
- sequencing targets.
+ The Short Sequence Assembly by K-mer search and 3' read Extension
+ (SSAKE) is a genomics application for aggressively assembling
+ millions of short nucleotide sequences by progressively searching for
+ perfect 3'-most k-mers using a DNA prefix tree. SSAKE is designed to
+ help leverage the information from short sequences reads by
+ stringently clustering them into contigs that can be used to
+ characterize novel sequencing targets.
Package: ssake-examples
-Architecture: any
+Architecture: all
Depends: ssake
Description: assembling millions of very short DNA sequences
- SSAKE is a genomics application for assembling millions of very short DNA sequences.
+ SSAKE is a genomics application for assembling millions of very short
+ DNA sequences.
.
- The Short Sequence Assembly by K-mer search and 3' read Extension (SSAKE) is a
- genomics application for aggressively assembling millions of short nucleotide
- sequences by progressively searching for perfect 3'-most k-mers using a DNA prefix
- tree. SSAKE is designed to help leverage the information from short sequences reads
- by stringently clustering them into contigs that can be used to characterize novel
- sequencing targets.
+ The Short Sequence Assembly by K-mer search and 3' read Extension
+ (SSAKE) is a genomics application for aggressively assembling
+ millions of short nucleotide sequences by progressively searching for
+ perfect 3'-most k-mers using a DNA prefix tree. SSAKE is designed to
+ help leverage the information from short sequences reads by
+ stringently clustering them into contigs that can be used to
+ characterize novel sequencing targets.
.
This package contains test sequences provided by upstream.
Modified: trunk/packages/ssake/trunk/debian/copyright
===================================================================
--- trunk/packages/ssake/trunk/debian/copyright 2008-11-24 12:33:30 UTC (rev 2727)
+++ trunk/packages/ssake/trunk/debian/copyright 2008-11-24 13:15:58 UTC (rev 2728)
@@ -6,7 +6,7 @@
Files: *
License: GPL2+
-Copyright: © 2003-2008 Heng Li <lh3 at sanger.ac.uk>
+Copyright: © 2006-2008 Rene Warren <rwarren at bcgsc.ca>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 2 of the License, or
Modified: trunk/packages/ssake/trunk/debian/rules
===================================================================
--- trunk/packages/ssake/trunk/debian/rules 2008-11-24 12:33:30 UTC (rev 2727)
+++ trunk/packages/ssake/trunk/debian/rules 2008-11-24 13:15:58 UTC (rev 2728)
@@ -3,4 +3,13 @@
# (C) Andreas Tille
# GPL
+pkg=ssake
+examples=$(pkg)-examples
+
include /usr/share/cdbs/1/rules/debhelper.mk
+
+install/$(pkg)::
+ cp -a SSAKE `pwd`/debian/$(pkg)/usr/bin/ssake
+
+install/$(examples)::
+ cp -a ssake_test/* `pwd`/debian/$(examples)/usr/share/doc/$(pkg)/examples
Added: trunk/packages/ssake/trunk/debian/ssake-examples.dirs
===================================================================
--- trunk/packages/ssake/trunk/debian/ssake-examples.dirs (rev 0)
+++ trunk/packages/ssake/trunk/debian/ssake-examples.dirs 2008-11-24 13:15:58 UTC (rev 2728)
@@ -0,0 +1 @@
+usr/share/doc/ssake/examples
Added: trunk/packages/ssake/trunk/debian/ssake.1
===================================================================
--- trunk/packages/ssake/trunk/debian/ssake.1 (rev 0)
+++ trunk/packages/ssake/trunk/debian/ssake.1 2008-11-24 13:15:58 UTC (rev 2728)
@@ -0,0 +1,57 @@
+.TH "SSAKE" "1" "January 2008"
+.SH "NAME"
+ssake \- assembling millions of very short DNA sequences
+
+.SH SYNOPSIS
+Progressive assembly of millions of short DNA sequences by k-mer search
+through a prefix tree and 3' extension.
+
+.SH "OPTIONS"
+.PP
+.IP \-f
+Fasta file containing all the [paired (\-p 1) / unpaired (\-p 0)] reads (required) \fBpaired reads must now be separated by ":"\fR
+.IP \-s
+Fasta file containing sequences to use as seeds exclusively (specify only if different from read set, optional)
+.IP \-m
+Minimum number of overlapping bases with the seed/contig during overhang consensus build up (default -m 16)
+.IP \-o
+Minimum number of reads needed to call a base during an extension (default \-o 3)
+.IP \-r
+Minimum base ratio used to accept a overhang consensus base (default \-r 0.7)
+.IP \-t
+Trim up to \-t base(s) on the contig end when all possibilities have been exhausted for an extension (default \-t 0)>
+.IP -p
+Paired-end reads used? (\-p 1=yes, \-p 0=no, default \-p 0)
+.IP \-v
+Runs in verbose mode (\-v 1=yes, \-v 0=no, default \-v 0, optional)
+.IP \-b
+Base name for your output files (optional)
+.PP
+============ Options below only considered with \-p 1 ============
+.IP \-d
+Mean distance expected/observed between paired-end reads (default \-d 200, optional)
+.IP -e
+Error (%) allowed on mean distance e.g. \-e 0.75 == distance +/- 75% (default \-e 0.75, optional)
+.IP \-k
+Minimum number of links (read pairs) to compute scaffold (default \-k 2, optional)
+.IP \-a
+Maximum link ratio between two best contig pairs *higher values lead to least accurate scaffolding* (default \-a 0.70, optional)
+.IP \-z
+Minimum contig size to track paired-end reads (default \-z 50, optional)
+.IP \-g
+Fasta file containing unpaired sequence reads (optional)
+
+.SH SEE ALSO
+/usr/share/doc/ssake/SSAKE.readmee between pairing reads are used interchangeably
+
+.SH "AUTHORS"
+.PP
+This manual page was written by Andreas Tille <tille at debian.org> for
+the \fBDebian\fP system (but may be used by others). Permission is
+granted to copy, distribute and/or modify this document under
+the terms of the GNU General Public License, Version 2 any
+later version published by the Free Software Foundation.
+
+.PP
+On Debian systems, the complete text of the GNU General Public
+License can be found in /usr/share/common-licenses/GPL.
Added: trunk/packages/ssake/trunk/debian/ssake.dirs
===================================================================
--- trunk/packages/ssake/trunk/debian/ssake.dirs (rev 0)
+++ trunk/packages/ssake/trunk/debian/ssake.dirs 2008-11-24 13:15:58 UTC (rev 2728)
@@ -0,0 +1 @@
+usr/bin
Added: trunk/packages/ssake/trunk/debian/ssake.manpages
===================================================================
--- trunk/packages/ssake/trunk/debian/ssake.manpages (rev 0)
+++ trunk/packages/ssake/trunk/debian/ssake.manpages 2008-11-24 13:15:58 UTC (rev 2728)
@@ -0,0 +1 @@
+debian/ssake.1
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