[med-svn] r12824 - trunk/packages/zalign/trunk/debian

Tue Jan 22 16:53:35 UTC 2013

Author: tille
Date: 2013-01-22 16:53:35 +0000 (Tue, 22 Jan 2013)
New Revision: 12824

Added:
   trunk/packages/zalign/trunk/debian/manpages
   trunk/packages/zalign/trunk/debian/mpialign.1
   trunk/packages/zalign/trunk/debian/zalign.1
Modified:
   trunk/packages/zalign/trunk/debian/changelog
   trunk/packages/zalign/trunk/debian/compat
   trunk/packages/zalign/trunk/debian/control
   trunk/packages/zalign/trunk/debian/copyright
Log:
Poilishing; added manpages; Remark: both executables are issuing the very same text when using '-h' option - so the help2man created manpages are the same which does not seem to be correct.


Modified: trunk/packages/zalign/trunk/debian/changelog
===================================================================

--- trunk/packages/zalign/trunk/debian/changelog	2013-01-22 13:13:31 UTC (rev 12823)
+++ trunk/packages/zalign/trunk/debian/changelog	2013-01-22 16:53:35 UTC (rev 12824)
@@ -2,4 +2,4 @@
 
   * Initial release (Closes: #686000)
 
- -- Steffen Moeller <moeller at debian.org>  Mon, 27 Aug 2012 15:14:15 +0200
+ -- Steffen Moeller <moeller at debian.org>  Tue, 22 Jan 2013 17:21:13 +0100

Modified: trunk/packages/zalign/trunk/debian/compat
===================================================================
--- trunk/packages/zalign/trunk/debian/compat	2013-01-22 13:13:31 UTC (rev 12823)
+++ trunk/packages/zalign/trunk/debian/compat	2013-01-22 16:53:35 UTC (rev 12824)
@@ -1 +1 @@
-8
+9

Modified: trunk/packages/zalign/trunk/debian/control
===================================================================
--- trunk/packages/zalign/trunk/debian/control	2013-01-22 13:13:31 UTC (rev 12823)
+++ trunk/packages/zalign/trunk/debian/control	2013-01-22 16:53:35 UTC (rev 12824)
@@ -1,9 +1,11 @@
 Source: zalign
 Section: science
 Priority: optional
-Maintainer: Steffen Moeller <moeller at debian.org>
-Build-Depends: debhelper (>= 8.0.0), autotools-dev, libopenmpi-dev
-Standards-Version: 3.9.3
+Maintainer:  Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <moeller at debian.org>,
+           Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 9), autotools-dev, libopenmpi-dev
+Standards-Version: 3.9.4
 Homepage: https://launchpad.net/zalign
 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/zalign/trunk/
 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/zalign/trunk

Modified: trunk/packages/zalign/trunk/debian/copyright
===================================================================
--- trunk/packages/zalign/trunk/debian/copyright	2013-01-22 13:13:31 UTC (rev 12823)
+++ trunk/packages/zalign/trunk/debian/copyright	2013-01-22 16:53:35 UTC (rev 12824)
@@ -1,11 +1,10 @@
-Format: http://dep.debian.net/deps/dep5
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: zalign
 Source: https://launchpad.net/zalign
 
 Files: *
 Copyright: 2006-2009 Rodolfo Bezerra Batista <rodolfo.batista at gmail.com>
-	   2006-2009 Felipe Brant Scarel <fbscarel at gmail.com>
-
+    2006-2009 Felipe Brant Scarel <fbscarel at gmail.com>
 License: GPL-3.0+
 
 Files: debian/*
@@ -28,3 +27,4 @@
  .
  On Debian systems, the complete text of the GNU General
  Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
+

Added: trunk/packages/zalign/trunk/debian/manpages
===================================================================
--- trunk/packages/zalign/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/zalign/trunk/debian/manpages	2013-01-22 16:53:35 UTC (rev 12824)
@@ -0,0 +1 @@
+debian/*.1

Added: trunk/packages/zalign/trunk/debian/mpialign.1
===================================================================
--- trunk/packages/zalign/trunk/debian/mpialign.1	                        (rev 0)
+++ trunk/packages/zalign/trunk/debian/mpialign.1	2013-01-22 16:53:35 UTC (rev 12824)
@@ -0,0 +1,44 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.10.
+.TH MPIALIGN "1" "16. Aug 2009" "0.9.1" "User Commands"
+.SH NAME
+mpialign \- parallel local alignment of biological sequences
+.SH SYNOPSIS
+.B
+mpialign
+[\-s scores] [\-S split] [\-H hblk] [\-V vblk] file1 file2
+.SH DESCRIPTION
+mpiAlign is a local sequence aligner, especially intended for use with
+large biological DNA sequences, with more than 1Mbp (Millions of base
+pairs). It uses the Smith-Waterman exact algorithm with affine gap cost
+function to perform this task.
+.SS "General options:"
+.TP
+\fB\-h\fR
+display this help and exit
+.TP
+\fB\-s\fR <scores>
+specify a comma\-separated list of scores to be used while
+calculating aligment matrices throughout the program. The list
+must be in the format "\-sMATCH,MISMATCH,GAP_OPEN,GAP_EXTENSION"
+(without quotes), and is parsed in this PRECISE order; no spaces
+are allowed between values. If there are any unspecified
+parameters, these are set to default values and a warning message
+is issued; exceeding parameters are discarded
+.SS "Stage 2 options:"
+.TP
+\fB\-S\fR <split>
+(mpialign only) number of parts in which to split the alignment
+matrix; after this step a cyclic block model is applied,
+subdividing each part equally between all available nodes
+.TP
+\fB\-H\fR <hblk>
+(mpialign only) number of horizontal subdivisions made by each
+node to its alignment submatrix; since this value defines block
+width, a good choice should allow two full matrix lines to fit
+the processor's cache pages, improving algorithm performance
+.TP
+\fB\-V\fR <vblk>
+(mpialign only) number of vertical subdivisions made by each node
+to its alignment submatrix; this value directly affects the
+amount of internode communication and is used ONLY if 'split' is
+set to 1, otherwise it is set to the number of available nodes

Added: trunk/packages/zalign/trunk/debian/zalign.1
===================================================================
--- trunk/packages/zalign/trunk/debian/zalign.1	                        (rev 0)
+++ trunk/packages/zalign/trunk/debian/zalign.1	2013-01-22 16:53:35 UTC (rev 12824)
@@ -0,0 +1,44 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.40.10.
+.TH ZALIGN "1" "16. Aug 2009" "0.9.1" "User Commands"
+.SH NAME
+zalign \- parallel local alignment of biological sequences
+.SH SYNOPSIS
+.B
+zalign
+[\-s scores] [\-S split] [\-H hblk] [\-V vblk] file1 file2
+.SH DESCRIPTION
+zAlign is a local sequence aligner, especially intended for use with
+large biological DNA sequences, with more than 1Mbp (Millions of base
+pairs). It uses the Smith-Waterman exact algorithm with affine gap cost
+function to perform this task.
+.SS "General options:"
+.TP
+\fB\-h\fR
+display this help and exit
+.TP
+\fB\-s\fR <scores>
+specify a comma\-separated list of scores to be used while
+calculating aligment matrices throughout the program. The list
+must be in the format "\-sMATCH,MISMATCH,GAP_OPEN,GAP_EXTENSION"
+(without quotes), and is parsed in this PRECISE order; no spaces
+are allowed between values. If there are any unspecified
+parameters, these are set to default values and a warning message
+is issued; exceeding parameters are discarded
+.SS "Stage 2 options:"
+.TP
+\fB\-S\fR <split>
+(mpialign only) number of parts in which to split the alignment
+matrix; after this step a cyclic block model is applied,
+subdividing each part equally between all available nodes
+.TP
+\fB\-H\fR <hblk>
+(mpialign only) number of horizontal subdivisions made by each
+node to its alignment submatrix; since this value defines block
+width, a good choice should allow two full matrix lines to fit
+the processor's cache pages, improving algorithm performance
+.TP
+\fB\-V\fR <vblk>
+(mpialign only) number of vertical subdivisions made by each node
+to its alignment submatrix; this value directly affects the
+amount of internode communication and is used ONLY if 'split' is
+set to 1, otherwise it is set to the number of available nodes


