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 <[email protected]> Mon, 27 Aug 2012 15:14:15 +0200 + -- Steffen Moeller <[email protected]> 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 <[email protected]> -Build-Depends: debhelper (>= 8.0.0), autotools-dev, libopenmpi-dev -Standards-Version: 3.9.3 +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Steffen Moeller <[email protected]>, + Andreas Tille <[email protected]> +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 <[email protected]> - 2006-2009 Felipe Brant Scarel <[email protected]> - + 2006-2009 Felipe Brant Scarel <[email protected]> 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 _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
