[Pkg-emboss-commits] r103 - / embassy-domainatrix embassy-domainatrix/trunk embassy-domainatrix/trunk/debian embassy-domainatrix/trunk/debian/manpages embassy-domainatrix/trunk/debian/patches
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Tue Sep 25 17:11:23 UTC 2007
Author: charles-guest
Date: 2007-09-25 17:11:23 +0000 (Tue, 25 Sep 2007)
New Revision: 103
Added:
embassy-domainatrix/
embassy-domainatrix/trunk/
embassy-domainatrix/trunk/debian/
embassy-domainatrix/trunk/debian/changelog
embassy-domainatrix/trunk/debian/control
embassy-domainatrix/trunk/debian/copyright
embassy-domainatrix/trunk/debian/embassy-domainatrix.manpages
embassy-domainatrix/trunk/debian/manpages/
embassy-domainatrix/trunk/debian/manpages/cathparse.1
embassy-domainatrix/trunk/debian/manpages/domainnr.1
embassy-domainatrix/trunk/debian/manpages/domainreso.1
embassy-domainatrix/trunk/debian/manpages/domainseqs.1
embassy-domainatrix/trunk/debian/manpages/domainsse.1
embassy-domainatrix/trunk/debian/manpages/libscanout.1
embassy-domainatrix/trunk/debian/manpages/scopparse.1
embassy-domainatrix/trunk/debian/manpages/ssematch.1
embassy-domainatrix/trunk/debian/patches/
embassy-domainatrix/trunk/debian/patches/usr-include-ajax-nucleus.patch
embassy-domainatrix/trunk/debian/rules
embassy-domainatrix/trunk/debian/watch
Log:
[embassy-domainatrix] Preliminary package, still FTBFSes.
Property changes on: embassy-domainatrix/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: embassy-domainatrix/trunk/debian/changelog
===================================================================
--- embassy-domainatrix/trunk/debian/changelog (rev 0)
+++ embassy-domainatrix/trunk/debian/changelog 2007-09-25 17:11:23 UTC (rev 103)
@@ -0,0 +1,5 @@
+embassy-domainatrix (0.1.0-1) unstable; urgency=low
+
+ * Initial release
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Tue, 25 Sep 2007 13:52:47 +0900
Added: embassy-domainatrix/trunk/debian/control
===================================================================
--- embassy-domainatrix/trunk/debian/control (rev 0)
+++ embassy-domainatrix/trunk/debian/control 2007-09-25 17:11:23 UTC (rev 103)
@@ -0,0 +1,27 @@
+Source: embassy-domainatrix
+Section: science
+Priority: optional
+Build-depends: cdbs, debhelper (>= 5), libajax5-dev, libnucleus5-dev, emboss-lib
+Maintainer: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
+Uploaders: Charles Plessy <charles-debian-nospam at plessy.org>
+XS-Vcs-Browser: http://svn.debian.org/wsvn/pkg-emboss/embassy-domainatrix/trunk/debian
+XS-Vcs-Svn: svn://svn.debian.org/svn/pkg-emboss/embassy-domainatrix
+Standards-Version: 3.7.2
+Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMAINATRIX
+
+Package: embassy-domainatrix
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: emboss
+Suggests: embassy
+Description: Extra EMBOSS commands to handle domain classification file
+ The DOMAINATRIX programs were developed by Jon Ison and colleagues at MRC HGMP
+ for their protein domain research. They are included as an EMBASSY package as
+ a work in progress.
+ .
+ Applications in the current domainatrix release are cathparse (generates DCF
+ file from raw CATH files), domainnr (removes redundant domains from a DCF
+ file), domainreso (removes low resolution domains from a DCF file), domainseqs
+ (adds sequence records to a DCF file), domainsse (adds secondary structure
+ records to a DCF file), scopparse (generates DCF file from raw SCOP files) and
+ ssematch (searches a DCF file for secondary structure matches).
Added: embassy-domainatrix/trunk/debian/copyright
===================================================================
--- embassy-domainatrix/trunk/debian/copyright (rev 0)
+++ embassy-domainatrix/trunk/debian/copyright 2007-09-25 17:11:23 UTC (rev 103)
@@ -0,0 +1,44 @@
+This package was debianized by Charles Plessy
+<charles-debian-nospam at plessy.org> on Tue, 25 Sep 2007 13:01:56 +0900.
+
+It was downloaded from <ftp://emboss.open-bio.org/pub/EMBOSS/>
+
+Upstream Authors (alphabetical):
+
+ Alan Bleasby (ableasby at ebi.ac.uk)
+ Matt Blades
+ Mike Hurley
+ Jon Ison (jison at ebi.ac.uk)
+ Amanda O'Reilly
+ Ranjeeva Ranasinghe
+
+Copyright 2007 the upstream authors.
+
+License:
+
+ This package 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
+ (at your option) any later version.
+
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL'.
+
+
+Please cite the authors and EMBOSS.
+
+ Rice P, Bleasby A.J. 2000. EMBOSS - The European Molecular Biology Open
+ Software Suite. Trends in Genetics, 15:276-278.
+
+
+The Debian packaging is copyright 2007 Charles Plessy and
+is licensed under the same terms as domainatrix, see above.
Added: embassy-domainatrix/trunk/debian/embassy-domainatrix.manpages
===================================================================
--- embassy-domainatrix/trunk/debian/embassy-domainatrix.manpages (rev 0)
+++ embassy-domainatrix/trunk/debian/embassy-domainatrix.manpages 2007-09-25 17:11:23 UTC (rev 103)
@@ -0,0 +1,9 @@
+debian/manpages/cathparse.1
+debian/manpages/domainnr.1
+debian/manpages/domainreso.1
+debian/manpages/domainseqs.1
+debian/manpages/domainsse.1
+debian/manpages/libscan.1
+debian/manpages/libscanout.1
+debian/manpages/scopparse.1
+debian/manpages/ssematch.1
Added: embassy-domainatrix/trunk/debian/manpages/cathparse.1
===================================================================
--- embassy-domainatrix/trunk/debian/manpages/cathparse.1 (rev 0)
+++ embassy-domainatrix/trunk/debian/manpages/cathparse.1 2007-09-25 17:11:23 UTC (rev 103)
@@ -0,0 +1,71 @@
+.\" Title: CATHPARSE
+.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 09/25/2007
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 0.1.0
+.\"
+.TH "CATHPARSE" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+cathparse - Generates DCF file from raw CATH files.
+.SH "SYNOPSIS"
+.HP 10
+\fBcathparse\fR \fB\-listfile\ \fR\fB\fIinfile\fR\fR \fB\-domfile\ \fR\fB\fIinfile\fR\fR \fB\-namesfile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP 10
+\fBcathparse\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcathparse\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "Utils:Database creation" command group(s)\.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-listfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of raw CATH classification file (caths\.list\.vX\.X) (input)\. The raw CATH parsable files (classification and description files) available from ftp\.biochem\.ucl\.ac\.uk (/pub/cathdata/v2\.4)\. Default value: caths\.list\.v2\.4
+.RE
+.PP
+\fB\-domfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of raw CATH classification file (domlist\.vX\.X) (input)\. The raw CATH parsable files (classification and description files) available from ftp\.biochem\.ucl\.ac\.uk (/pub/cathdata/v2\.4)\. Default value: domlist\.v2\.4
+.RE
+.PP
+\fB\-namesfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of raw CATH classification file (CAT\.names\.all\.vX\.X) (input)\. The raw CATH parsable files (classification and description files) available from ftp\.biochem\.ucl\.ac\.uk (/pub/cathdata/v2\.4)\. Default value: CAT\.names\.all\.v2\.4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of CATH DCF file (domain classification file) (output)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\. Default value: Ecath\.dat
+.RE
+.PP
+\fB\-logfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of the CATHPARSE log file\. Default value: cathparse\.log
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\.debian\.org/emboss), or directly to the EMBOSS developers (http://sourceforge\.net/tracker/?group_id=93650&atid=605031)\.
+.SH "SEE ALSO"
+.PP
+cathparse is fully documented via the
+\fBtfm\fR(1)
+system\.
+.SH "AUTHOR"
+.PP
+\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists\.alioth\.debian\.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian EMBOSS Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\. It can be redistributed under the same terms as EMBOSS itself\.
+.sp
Added: embassy-domainatrix/trunk/debian/manpages/domainnr.1
===================================================================
--- embassy-domainatrix/trunk/debian/manpages/domainnr.1 (rev 0)
+++ embassy-domainatrix/trunk/debian/manpages/domainnr.1 2007-09-25 17:11:23 UTC (rev 103)
@@ -0,0 +1,114 @@
+.\" Title: DOMAINNR
+.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 09/25/2007
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 0.1.0
+.\"
+.TH "DOMAINNR" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+domainnr - Removes redundant domains from a DCF file.
+.SH "SYNOPSIS"
+.HP 9
+\fBdomainnr\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-retain\ \fR\fB\fItoggle\fR\fR \fB\-node\ \fR\fB\fIlist\fR\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-threshlow\ \fR\fB\fIfloat\fR\fR \fB\-threshup\ \fR\fB\fIfloat\fR\fR [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-redoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP 9
+\fBdomainnr\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdomainnr\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "Utils:Database creation" command group(s)\.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dcfinfile\fR \fIinfile\fR
+.RS 4
+This option specifies name of DCF file (domain classification file) (input)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\.
+.RE
+.PP
+\fB\-datafile\fR \fImatrixf\fR
+.RS 4
+This option specifies the residue substitution matrix\. This is used for sequence comparison\. Default value: EBLOSUM62
+.RE
+.PP
+\fB\-retain\fR \fItoggle\fR
+.RS 4
+This option specifies whether to write redundant domains to a separate file\. If this option is selected, redundant domains are written to a separate output file\. Default value: N
+.RE
+.SS "Required section"
+.PP
+\fB\-node\fR \fIlist\fR
+.RS 4
+This option specifies the node for redundancy removal\. Redundancy can be removed at any specified node in the SCOP or CATH hierarchies\. For example by selecting \'Class\' entries belonging to the same Class will be non\-redundant\. Default value: 1
+.RE
+.PP
+\fB\-mode\fR \fIlist\fR
+.RS 4
+This option specifies whether to remove redundancy at a single threshold % sequence similarity or remove redundancy outside a range of acceptable threshold % similarity\. All permutations of pair\-wise sequence alignments are calculated for each domain family in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm\. Redundant sequences are removed in one of two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded\. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded\. Default value: 1
+.RE
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded\. Default value: 95\.0
+.RE
+.PP
+\fB\-threshlow\fR \fIfloat\fR
+.RS 4
+This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\. Default value: 30\.0
+.RE
+.PP
+\fB\-threshup\fR \fIfloat\fR
+.RS 4
+This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\. Default value: 90\.0
+.RE
+.SS "Additional section"
+.PP
+\fB\-gapopen\fR \fIfloat\fR
+.RS 4
+This option specifies the gap insertion penalty\. This is the score taken away when a gap is created\. The best value depends on the choice of comparison matrix\. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\. Default value: 10
+.RE
+.PP
+\fB\-gapextend\fR \fIfloat\fR
+.RS 4
+This option specifies the gap extension penalty\. This is added to the standard gap penalty for each base or residue in the gap\. This is how long gaps are penalized\. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\. Default value: 0\.5
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-dcfoutfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of non\-redundant DCF file (domain classification file) (output)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\. Default value: test\.scop
+.RE
+.PP
+\fB\-redoutfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of DCF file (domain classification file) for redundant sequences (output)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\.
+.RE
+.PP
+\fB\-logfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of log file for the build\. The log file contains messages about any errors arising while domainnr ran\. Default value: domainnr\.log
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\.debian\.org/emboss), or directly to the EMBOSS developers (http://sourceforge\.net/tracker/?group_id=93650&atid=605031)\.
+.SH "SEE ALSO"
+.PP
+domainnr is fully documented via the
+\fBtfm\fR(1)
+system\.
+.SH "AUTHOR"
+.PP
+\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists\.alioth\.debian\.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian EMBOSS Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\. It can be redistributed under the same terms as EMBOSS itself\.
+.sp
Added: embassy-domainatrix/trunk/debian/manpages/domainreso.1
===================================================================
--- embassy-domainatrix/trunk/debian/manpages/domainreso.1 (rev 0)
+++ embassy-domainatrix/trunk/debian/manpages/domainreso.1 2007-09-25 17:11:23 UTC (rev 103)
@@ -0,0 +1,67 @@
+.\" Title: DOMAINRESO
+.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 09/25/2007
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 0.1.0
+.\"
+.TH "DOMAINRESO" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+domainreso - Remove low resolution domains from a DCF file.
+.SH "SYNOPSIS"
+.HP 11
+\fBdomainreso\fR \fB\-cpdbpath\ \fR\fB\fIdirlist\fR\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR
+.HP 11
+\fBdomainreso\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdomainreso\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "PROTEIN:3D STRUCTURE" command group(s)\.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-cpdbpath\fR \fIdirlist\fR
+.RS 4
+This option specifies the location of domain CCF file (clean coordinate files) (input)\. A \'clean cordinate file\' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL\-like)\. The files, generated by using PDBPARSE (pdb files) or DOMAINER (domains), contain \'cleaned\-up\' data that is self\-consistent and error\-corrected\. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\. Default value: \./
+.RE
+.PP
+\fB\-dcfinfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of DCF file (domain classification file) (input)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\.
+.RE
+.SS "Required section"
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+This option specifies the threshold for inclusion (Angstroms)\. Domains exceeding the threshold for inclusion (Angstroms) will not be given in the output file\. Default value: 2\.8
+.RE
+.SS "Output section"
+.PP
+\fB\-dcfoutfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of DCF file (domain classification file) (output)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\. Default value: test\.scop
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\.debian\.org/emboss), or directly to the EMBOSS developers (http://sourceforge\.net/tracker/?group_id=93650&atid=605031)\.
+.SH "SEE ALSO"
+.PP
+domainreso is fully documented via the
+\fBtfm\fR(1)
+system\.
+.SH "AUTHOR"
+.PP
+\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists\.alioth\.debian\.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian EMBOSS Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\. It can be redistributed under the same terms as EMBOSS itself\.
+.sp
Added: embassy-domainatrix/trunk/debian/manpages/domainseqs.1
===================================================================
--- embassy-domainatrix/trunk/debian/manpages/domainseqs.1 (rev 0)
+++ embassy-domainatrix/trunk/debian/manpages/domainseqs.1 2007-09-25 17:11:23 UTC (rev 103)
@@ -0,0 +1,93 @@
+.\" Title: DOMAINSEQS
+.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 09/25/2007
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 0.1.0
+.\"
+.TH "DOMAINSEQS" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+domainseqs - Adds sequence records to a DCF file.
+.SH "SYNOPSIS"
+.HP 11
+\fBdomainseqs\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-dpdbdir\ \fR\fB\fIdirectory\fR\fR \fB\-getswiss\ \fR\fB\fItoggle\fR\fR \fB\-pdbtospfile\ \fR\fB\fIinfile\fR\fR \fB\-datafile\ \fR\fB\fImatrixf\fR\fR \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP 11
+\fBdomainseqs\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdomainseqs\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "Utils:Database creation" command group(s)\.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dcfinfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of DCF file (domain classification file) (input)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\.
+.RE
+.PP
+\fB\-dpdbdir\fR \fIdirectory\fR
+.RS 4
+This option specifies the location of domain CCF file (clean coordinate files) (input)\. A \'clean cordinate file\' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL\-like)\. The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain \'cleaned\-up\' data that is self\-consistent and error\-corrected\. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\. Default value: \./
+.RE
+.PP
+\fB\-getswiss\fR \fItoggle\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-pdbtospfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of the pdbcodes to swissprot indexing file\. The swissprot:PDB equivalence file is generated by PDBTOSP
+.RE
+.PP
+\fB\-datafile\fR \fImatrixf\fR
+.RS 4
+This option specifies the residue substitution matrix, which is used for sequence comparison\. Default value: EBLOSUM62
+.RE
+.SS "Required section"
+.SS "Additional section"
+.PP
+\fB\-gapopen\fR \fIfloat\fR
+.RS 4
+This option specifies the gap insertion penalty\. This is the score taken away when a gap is created\. The best value depends on the choice of comparison matrix\. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\. Default value: 10
+.RE
+.PP
+\fB\-gapextend\fR \fIfloat\fR
+.RS 4
+This option specifies the gap extension penalty\. This is added to the standard gap penalty for each base or residue in the gap\. This is how long gaps are penalized\. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\. Default value: 0\.5
+.RE
+.SS "Output section"
+.PP
+\fB\-dcfoutfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of DCF file (domain classification file) (output)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\. Default value: domainseqs\.out
+.RE
+.PP
+\fB\-logfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of log file for the build\. The log file contains messages about any errors arising while domainseqs ran\. Default value: domainseqs\.log
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\.debian\.org/emboss), or directly to the EMBOSS developers (http://sourceforge\.net/tracker/?group_id=93650&atid=605031)\.
+.SH "SEE ALSO"
+.PP
+domainseqs is fully documented via the
+\fBtfm\fR(1)
+system\.
+.SH "AUTHOR"
+.PP
+\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists\.alioth\.debian\.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian EMBOSS Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\. It can be redistributed under the same terms as EMBOSS itself\.
+.sp
Added: embassy-domainatrix/trunk/debian/manpages/domainsse.1
===================================================================
--- embassy-domainatrix/trunk/debian/manpages/domainsse.1 (rev 0)
+++ embassy-domainatrix/trunk/debian/manpages/domainsse.1 2007-09-25 17:11:23 UTC (rev 103)
@@ -0,0 +1,68 @@
+.\" Title: DOMAINSSE
+.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 09/25/2007
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 0.1.0
+.\"
+.TH "DOMAINSSE" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+domainsse - Add secondary structure records to a DCF file.
+.SH "SYNOPSIS"
+.HP 10
+\fBdomainsse\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-dccfdir\ \fR\fB\fIdirectory\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP 10
+\fBdomainsse\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdomainsse\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "Utils:Database creation" command group(s)\.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dcfinfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of the DCF file (domain classification file) (input)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\.
+.RE
+.PP
+\fB\-dccfdir\fR \fIdirectory\fR
+.RS 4
+This option specifies the location of the domain CCF file (clean coordinate files) (input)\. A \'clean cordinate file\' contains protein coordinate and derived data for a single PDB file (\'protein clean coordinate file\') or a single domain from SCOP or CATH (\'domain clean coordinate file\'), in CCF format (EMBL\-like)\. The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain \'cleaned\-up\' data that is self\-consistent and error\-corrected\. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\. Default value: \./
+.RE
+.SS "Required section"
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-dcfoutfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of the DCF file (domain classification file) with secondary structure records (output)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\.
+.RE
+.PP
+\fB\-logfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of the DOMAINSSE log file\. Default value: domainsse\.log
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\.debian\.org/emboss), or directly to the EMBOSS developers (http://sourceforge\.net/tracker/?group_id=93650&atid=605031)\.
+.SH "SEE ALSO"
+.PP
+domainsse is fully documented via the
+\fBtfm\fR(1)
+system\.
+.SH "AUTHOR"
+.PP
+\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists\.alioth\.debian\.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian EMBOSS Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\. It can be redistributed under the same terms as EMBOSS itself\.
+.sp
Added: embassy-domainatrix/trunk/debian/manpages/libscanout.1
===================================================================
--- embassy-domainatrix/trunk/debian/manpages/libscanout.1 (rev 0)
+++ embassy-domainatrix/trunk/debian/manpages/libscanout.1 2007-09-25 17:11:23 UTC (rev 103)
@@ -0,0 +1,57 @@
+.\" Title: LIBSCANOUT
+.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 09/25/2007
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 0.1.0
+.\"
+.TH "LIBSCANOUT" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+libscanout - Reads a DHF file and writes a file of top-scoring Classes, Folds and Superfamilies.
+.SH "SYNOPSIS"
+.HP 11
+\fBlibscanout\fR \fB\-dhfinfile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP 11
+\fBlibscanout\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBlibscanout\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "Protein:3D Structure" command group(s)\.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dhfinfile\fR \fIinfile\fR
+.RS 4
+This option specifies the location of the DHF file (domain hits file) (input)\. A \'domain hits file\' contains database hits (sequences) with domain classification information, in FASTA or EMBL formats\. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\.
+.RE
+.SS "Required section"
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the location of the summary file (output)\. The summary file contains lists of domain Classes, Superfamilies and Families rank\-ordered on the basis of score (highest\-scoring first)\.
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\.debian\.org/emboss), or directly to the EMBOSS developers (http://sourceforge\.net/tracker/?group_id=93650&atid=605031)\.
+.SH "SEE ALSO"
+.PP
+libscanout is fully documented via the
+\fBtfm\fR(1)
+system\.
+.SH "AUTHOR"
+.PP
+\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists\.alioth\.debian\.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian EMBOSS Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\. It can be redistributed under the same terms as EMBOSS itself\.
+.sp
Added: embassy-domainatrix/trunk/debian/manpages/scopparse.1
===================================================================
--- embassy-domainatrix/trunk/debian/manpages/scopparse.1 (rev 0)
+++ embassy-domainatrix/trunk/debian/manpages/scopparse.1 2007-09-25 17:11:23 UTC (rev 103)
@@ -0,0 +1,78 @@
+.\" Title: SCOPPARSE
+.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 09/25/2007
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 0.1.0
+.\"
+.TH "SCOPPARSE" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+scopparse - Generate DCF file from raw SCOP files.
+.SH "SYNOPSIS"
+.HP 10
+\fBscopparse\fR \fB\-classfile\ \fR\fB\fIinfile\fR\fR \fB\-desinfile\ \fR\fB\fIinfile\fR\fR \fB\-nosegments\ \fR\fB\fIboolean\fR\fR \fB\-nomultichain\ \fR\fB\fIboolean\fR\fR [\fB\-nominor\ \fR\fB\fIboolean\fR\fR] \fB\-dcffile\ \fR\fB\fIoutfile\fR\fR
+.HP 10
+\fBscopparse\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBscopparse\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "Utils:Database creation" command group(s)\.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-classfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of raw SCOP classification file dir\.cla\.scop\.txt_X\.XX (input)\. This is the raw SCOP classification file available at http://scop\.mrc\-lmb\.cam\.ac\.uk/scop/parse/dir\.cla\.scop\.txt_1\.57\.
+.RE
+.PP
+\fB\-desinfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of raw SCOP description file dir\.des\.scop\.txt_X\.XX (input)\. This is the raw SCOP description file available at http://scop\.mrc\-lmb\.cam\.ac\.uk/scop/parse/dir\.des\.scop\.txt_1\.57\.
+.RE
+.SS "Required section"
+.PP
+\fB\-nosegments\fR \fIboolean\fR
+.RS 4
+This option specifies whether to omit domains comprising of more than one segment\. This is necessary if a continuous residue sequence is required\. Default value: N
+.RE
+.PP
+\fB\-nomultichain\fR \fIboolean\fR
+.RS 4
+This option specifies whether to omit domains comprising segments from more than one chain\. This is necessary if a continuous residue sequence is required\. Default value: N
+.RE
+.SS "Additional section"
+.PP
+\fB\-nominor\fR \fIboolean\fR
+.RS 4
+This option specifies whether to omit domains from minor classes (defined as anything not in class \'All alpha proteins\', \'All beta proteins\', \'Alpha and beta proteins (a/b)\' or \'Alpha and beta proteins (a+b)\')\. This is necessary or appropriate for many analyses\. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-dcffile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of SCOP DCF file (domain classification file) (output)\. A \'domain classification file\' contains classification and other data for domains from the SCOP or CATH databases\. The file is generated by using DOMAINER and is in DCF format (EMBL\-like)\. Domain sequence information can be added to the file by using DOMAINSEQS\. Default value: test\.scop
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\.debian\.org/emboss), or directly to the EMBOSS developers (http://sourceforge\.net/tracker/?group_id=93650&atid=605031)\.
+.SH "SEE ALSO"
+.PP
+scopparse is fully documented via the
+\fBtfm\fR(1)
+system\.
+.SH "AUTHOR"
+.PP
+\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists\.alioth\.debian\.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian EMBOSS Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\. It can be redistributed under the same terms as EMBOSS itself\.
+.sp
Added: embassy-domainatrix/trunk/debian/manpages/ssematch.1
===================================================================
--- embassy-domainatrix/trunk/debian/manpages/ssematch.1 (rev 0)
+++ embassy-domainatrix/trunk/debian/manpages/ssematch.1 2007-09-25 17:11:23 UTC (rev 103)
@@ -0,0 +1,103 @@
+.\" Title: SSEMATCH
+.\" Author: Debian EMBOSS Packaging Team <pkg-emboss-devel at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
+.\" Date: 09/25/2007
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: EMBOSS 0.1.0
+.\"
+.TH "SSEMATCH" "1" "09/25/2007" "EMBOSS 0.1.0" "EMBOSS Manual for Debian"
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.SH "NAME"
+ssematch - Search a DCF file for secondary structure matches.
+.SH "SYNOPSIS"
+.HP 9
+\fBssematch\fR \fB\-ssinfile\ \fR\fB\fIinfile\fR\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-maxhits\ \fR\fB\fIinteger\fR\fR [\fB\-gapopenr\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextendr\ \fR\fB\fIfloat\fR\fR] [\fB\-gapopene\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextende\ \fR\fB\fIfloat\fR\fR] \fB\-outssfile\ \fR\fB\fIoutfile\fR\fR \fB\-outsefile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP 9
+\fBssematch\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBssematch\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\. It is part of the "Utils:Database creation" command group(s)\.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-ssinfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of the file of secondary structure (input)\.
+.RE
+.PP
+\fB\-dcfinfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of the DCF file (domain classification file) (input)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\. The files are generated by using SCOPPARSE and CATHPARSE\. Domain sequence information can be added to the file by using DOMAINSEQS\.
+.RE
+.PP
+\fB\-datafile\fR \fImatrixf\fR
+.RS 4
+This option specifies the secondary structure substitution matrix\. Default value: SSSUB
+.RE
+.SS "Required section"
+.PP
+\fB\-maxhits\fR \fIinteger\fR
+.RS 4
+This option specifies the number of top\-scoring matches to report\. Default value: 5
+.RE
+.SS "Additional section"
+.PP
+\fB\-gapopenr\fR \fIfloat\fR
+.RS 4
+This options specifies the gap insertion penalty for reside\-based alignment\. The gap insertion penalty is the score taken away when a gap is created\. The best value depends on the choice of comparison matrix\. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\. Default value: 10
+.RE
+.PP
+\fB\-gapextendr\fR \fIfloat\fR
+.RS 4
+This options specifies the gap extension penalty for residue\-based alignment\. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\. This is how long gaps are penalized\. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\. Default value: 0\.5
+.RE
+.PP
+\fB\-gapopene\fR \fIfloat\fR
+.RS 4
+This options specifies the gap insertion penalty for element\-based alignment\. The gap insertion penalty is the score taken away when a gap is created\. The best value depends on the choice of comparison matrix\. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\. Default value: 10
+.RE
+.PP
+\fB\-gapextende\fR \fIfloat\fR
+.RS 4
+This options specifies the gap extension penalty for secondary structure element\-based alignment\. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\. This is how long gaps are penalized\. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\. Default value: 0\.5
+.RE
+.SS "Output section"
+.PP
+\fB\-outssfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of the file containing top\-scoring domains for residue\-based alinnment (output)\.A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\.
+.RE
+.PP
+\fB\-outsefile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of the file containing top\-scoring domains for secondary structure element\-based alinnment (output)\. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\.
+.RE
+.PP
+\fB\-logfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of the ssematch log file (output)\. Default value: ssematch\.log
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\.debian\.org/emboss), or directly to the EMBOSS developers (http://sourceforge\.net/tracker/?group_id=93650&atid=605031)\.
+.SH "SEE ALSO"
+.PP
+ssematch is fully documented via the
+\fBtfm\fR(1)
+system\.
+.SH "AUTHOR"
+.PP
+\fBDebian EMBOSS Packaging Team\fR <\&pkg\-emboss\-devel at lists\.alioth\.debian\.org\&>
+.sp -1n
+.IP "" 4
+Wrote the script used to autogenerate this manual page\.
+.SH "COPYRIGHT"
+Copyright \(co 2007 Debian EMBOSS Packaging Team
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\. It can be redistributed under the same terms as EMBOSS itself\.
+.sp
Added: embassy-domainatrix/trunk/debian/patches/usr-include-ajax-nucleus.patch
===================================================================
--- embassy-domainatrix/trunk/debian/patches/usr-include-ajax-nucleus.patch (rev 0)
+++ embassy-domainatrix/trunk/debian/patches/usr-include-ajax-nucleus.patch 2007-09-25 17:11:23 UTC (rev 103)
@@ -0,0 +1,24 @@
+diff -pruN ./src_old/Makefile.am ./src/Makefile.am
+--- ./src_old/Makefile.am 2007-03-17 00:28:31.000000000 +0900
++++ ./src/Makefile.am 2007-09-25 13:57:27.000000000 +0900
+@@ -8,7 +8,7 @@ bin_PROGRAMS = cathparse domainnr domain
+ if LOCALLINK
+ INCLUDES = -I../../../plplot -I../../../ajax -I../../../nucleus
+ else
+-INCLUDES = -I${embprefix}/include -I${embprefix}/include/eplplot
++INCLUDES = -I${embprefix}/include -I${embprefix}/include/eplplot -I${embprefix}/include/ajax -I${embprefix}/include/nucleus
+ endif
+
+ if ISSHARED
+diff -pruN ./src_old/Makefile.in ./src/Makefile.in
+--- ./src_old/Makefile.in 2007-07-10 22:29:38.000000000 +0900
++++ ./src/Makefile.in 2007-09-25 13:57:45.000000000 +0900
+@@ -275,7 +275,7 @@ target_alias = @target_alias@
+ top_builddir = @top_builddir@
+ top_srcdir = @top_srcdir@
+ SUBDIRS =
+- at LOCALLINK_FALSE@INCLUDES = -I${embprefix}/include -I${embprefix}/include/eplplot
++ at LOCALLINK_FALSE@INCLUDES = -I${embprefix}/include -I${embprefix}/include/eplplot -I${embprefix}/include/ajax -I${embprefix}/include/nucleus
+ @LOCALLINK_TRUE at INCLUDES = -I../../../plplot -I../../../ajax -I../../../nucleus
+ @ISAIXIA64_FALSE@@ISSHARED_TRUE at AM_CFLAGS =
+ @ISAIXIA64_TRUE@@ISSHARED_TRUE@@LOCALLINK_FALSE at AM_CFLAGS = -Wl,-bdynamic -Wl,-brtl -L${embprefix}/lib -lnucleus -lajax -leplplot
Added: embassy-domainatrix/trunk/debian/rules
===================================================================
--- embassy-domainatrix/trunk/debian/rules (rev 0)
+++ embassy-domainatrix/trunk/debian/rules 2007-09-25 17:11:23 UTC (rev 103)
@@ -0,0 +1,5 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/autotools.mk
Property changes on: embassy-domainatrix/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: embassy-domainatrix/trunk/debian/watch
===================================================================
--- embassy-domainatrix/trunk/debian/watch (rev 0)
+++ embassy-domainatrix/trunk/debian/watch 2007-09-25 17:11:23 UTC (rev 103)
@@ -0,0 +1,2 @@
+version=3
+ftp://emboss.open-bio.org/pub/EMBOSS/DOMAINATRIX-(.*)\.tar\.gz debian uupdate
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