[med-svn] r5127 - in trunk/packages/embassy-domsearch/tags: . 0.1.0++20100721-1 0.1.0++20100721-1/debian 0.1.0++20100721-1/debian/manpages
Charles Plessy
plessy at alioth.debian.org
Wed Aug 11 11:38:05 UTC 2010
Author: plessy
Date: 2010-08-11 11:38:04 +0000 (Wed, 11 Aug 2010)
New Revision: 5127
Added:
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/changelog
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/control
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/embassy-domsearch.manpages
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqfraggle.1e
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqnr.1e
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqsearch.1e
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqsort.1e
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqwords.1e
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/rules
Removed:
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/changelog
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/control
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/embassy-domsearch.manpages
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqfraggle.1e
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqnr.1e
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqsearch.1e
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqsort.1e
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqwords.1e
trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/rules
Log:
[svn-buildpackage] Tagging embassy-domsearch 0.1.0++20100721-1
Property changes on: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1
___________________________________________________________________
Added: svn:mergeinfo
+
Deleted: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/changelog
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/changelog 2010-08-10 14:18:14 UTC (rev 5121)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/changelog 2010-08-11 11:38:04 UTC (rev 5127)
@@ -1,17 +0,0 @@
-embassy-domsearch (0.1.0++20100115-1) unstable; urgency=low
-
- * New upstream release in which the version number was unchanged.
- (I chose a strange version number to avoid an epoch because of
- the typo in the previous number).
- * debian/control:
- - Build against EMBOSS 6.2 (Closes: #587119).
- - Checked conformance with Policy 3.8.4 (no changes needed).
- * debian/*manpages* refreshed.
-
- -- Charles Plessy <plessy at debian.org> Sat, 26 Jun 2010 22:58:36 +0900
-
-embassy-domsearch (0.1.0+20980715-1) unstable; urgency=low
-
- * Initial release (Closes: #537204).
-
- -- Charles Plessy <plessy at debian.org> Mon, 20 Jul 2009 10:43:26 +0900
Copied: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/changelog (from rev 5126, trunk/packages/embassy-domsearch/trunk/debian/changelog)
===================================================================
--- trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/changelog (rev 0)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/changelog 2010-08-11 11:38:04 UTC (rev 5127)
@@ -0,0 +1,29 @@
+embassy-domsearch (0.1.0++20100721-1) unstable; urgency=low
+
+ * New upstream release in which the version number was unchanged.
+ * Build-Depends on emboss 6.3.1 (debian/control, debian/rules,
+ closes: #591121).
+ * Build-Depends on libmysqlclient-dev and libpq-dev until emboss is fixed.
+ * Pass -Wl,--as-needed to avoid unneeded binary dependencies (debian/rules).
+ * Incremented Standards-Version to reflect conformance with Policy 3.9.1
+ (debian/control, no changes needed).
+
+ -- Charles Plessy <plessy at debian.org> Wed, 11 Aug 2010 20:33:08 +0900
+
+embassy-domsearch (0.1.0++20100115-1) unstable; urgency=low
+
+ * New upstream release in which the version number was unchanged.
+ (I chose a strange version number to avoid an epoch because of
+ the typo in the previous number).
+ * debian/control:
+ - Build against EMBOSS 6.2 (Closes: #587119).
+ - Checked conformance with Policy 3.8.4 (no changes needed).
+ * debian/*manpages* refreshed.
+
+ -- Charles Plessy <plessy at debian.org> Sat, 26 Jun 2010 22:58:36 +0900
+
+embassy-domsearch (0.1.0+20980715-1) unstable; urgency=low
+
+ * Initial release (Closes: #537204).
+
+ -- Charles Plessy <plessy at debian.org> Mon, 20 Jul 2009 10:43:26 +0900
Deleted: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/control
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/control 2010-08-10 14:18:14 UTC (rev 5121)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/control 2010-08-11 11:38:04 UTC (rev 5127)
@@ -1,27 +0,0 @@
-Source: embassy-domsearch
-Section: science
-Priority: optional
-Build-Depends: cdbs, debhelper (>= 7), libajax6-dev (>= 6.2), libnucleus6-dev (>= 6.2), emboss-lib (>= 6.2), libx11-dev, libgd2-xpm-dev
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Charles Plessy <plessy at debian.org>
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/embassy-domsearch/trunk/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/embassy-domsearch/trunk/
-Standards-Version: 3.8.4
-Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMSEARCH
-
-Package: embassy-domsearch
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: emboss
-Suggests: embassy
-Description: Extra EMBOSS commands to search for protein domains
- The DOMSEARCH 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 this DOMSEARCH release are seqfraggle (removes fragment
- sequences from DHF files), seqnr (removes redundancy from DHF files), seqsearch
- (generates PSI-BLAST hits (DHF file) from a DAF file), seqsort (Remove
- ambiguous classified sequences from DHF files) and seqwords (Generates DHF
- files from keyword search of UniProt).
Copied: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/control (from rev 5126, trunk/packages/embassy-domsearch/trunk/debian/control)
===================================================================
--- trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/control (rev 0)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/control 2010-08-11 11:38:04 UTC (rev 5127)
@@ -0,0 +1,36 @@
+Source: embassy-domsearch
+Section: science
+Priority: optional
+Build-Depends:
+ cdbs,
+ debhelper (>= 7),
+ libajax6-dev (>= 6.3),
+ libnucleus6-dev (>= 6.3),
+ emboss-lib (>= 6.3),
+ libx11-dev,
+ libgd2-xpm-dev,
+ libmysqlclient-dev,
+ libpq-dev
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy at debian.org>
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/embassy-domsearch/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/embassy-domsearch/trunk/
+Standards-Version: 3.9.1
+Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMSEARCH
+
+Package: embassy-domsearch
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: emboss
+Suggests: embassy
+Description: Extra EMBOSS commands to search for protein domains
+ The DOMSEARCH 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 this DOMSEARCH release are seqfraggle (removes fragment
+ sequences from DHF files), seqnr (removes redundancy from DHF files), seqsearch
+ (generates PSI-BLAST hits (DHF file) from a DAF file), seqsort (Remove
+ ambiguous classified sequences from DHF files) and seqwords (Generates DHF
+ files from keyword search of UniProt).
Deleted: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/embassy-domsearch.manpages
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/embassy-domsearch.manpages 2010-08-10 14:18:14 UTC (rev 5121)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/embassy-domsearch.manpages 2010-08-11 11:38:04 UTC (rev 5127)
@@ -1,5 +0,0 @@
-debian/manpages/seqsort.1e
-debian/manpages/seqsearch.1e
-debian/manpages/seqwords.1e
-debian/manpages/seqfraggle.1e
-debian/manpages/seqnr.1e
Copied: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/embassy-domsearch.manpages (from rev 5126, trunk/packages/embassy-domsearch/trunk/debian/embassy-domsearch.manpages)
===================================================================
--- trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/embassy-domsearch.manpages (rev 0)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/embassy-domsearch.manpages 2010-08-11 11:38:04 UTC (rev 5127)
@@ -0,0 +1,5 @@
+debian/manpages/seqfraggle.1e
+debian/manpages/seqnr.1e
+debian/manpages/seqsearch.1e
+debian/manpages/seqsort.1e
+debian/manpages/seqwords.1e
Deleted: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqfraggle.1e
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqfraggle.1e 2010-08-10 14:18:14 UTC (rev 5121)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqfraggle.1e 2010-08-11 11:38:04 UTC (rev 5127)
@@ -1,78 +0,0 @@
-'\" t
-.\" Title: SEQFRAGGLE
-.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
-.\" Date: 06/26/2010
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0++20100115
-.\" Language: English
-.\"
-.TH "SEQFRAGGLE" "1e" "06/26/2010" "EMBOSS 0.1.0++20100115" "EMBOSS Manual for Debian"
-.\" -----------------------------------------------------------------
-.\" * Define some portability stuff
-.\" -----------------------------------------------------------------
-.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.\" http://bugs.debian.org/507673
-.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
-.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.ie \n(.g .ds Aq \(aq
-.el .ds Aq '
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
-.SH "NAME"
-seqfraggle \- Removes fragment sequences from DHF files\&.
-.SH "SYNOPSIS"
-.HP \w'\fBseqfraggle\fR\ 'u
-\fBseqfraggle\fR \fB\-dhfinpath\ \fR\fB\fIdirlist\fR\fR \fB\-thresh\ \fR\fB\fIinteger\fR\fR \fB\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR
-.HP \w'\fBseqfraggle\fR\ 'u
-\fBseqfraggle\fR \fB\-help\fR
-.SH "DESCRIPTION"
-.PP
-\fBseqfraggle\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\-dhfinpath\fR \fIdirlist\fR
-.RS 4
-This option specifies the location of DHF files (domain hits files) or other sequence files (input)\&. A \*(Aqdomain hits file\*(Aq 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\&. Alternatively, SEQFRAGGLE will accept sequence or sequence sets in any of the common formats\&. Default value: \&./
-.RE
-.SS "Required section"
-.PP
-\fB\-thresh\fR \fIinteger\fR
-.RS 4
-This option specifies the percentage of median length for definition of fragments\&. SEQFRAGGLE first determines the median length of all the sequences in the input file, then discards any hit sequences which are not within a threshold percentage of the median length\&. The remaining sequences are written to the output file\&. Default value: 50
-.RE
-.SS "Output section"
-.PP
-\fB\-dhfoutdir\fR \fIoutdir\fR
-.RS 4
-This option specifies the location of DHF files (domain hits files) (output)\&. A \*(Aqdomain hits file\*(Aq 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\&. Alternatively, SEQFRAGGLE will write output files in any of the common formats\&. Default value: \&./
-.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
-seqfraggle is fully documented via the
-\fBtfm\fR(1)
-system\&.
-.SH "AUTHOR"
-.PP
-\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.RS 4
-Wrote the script used to autogenerate this manual page\&.
-.RE
-.SH "COPYRIGHT"
-.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
Copied: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqfraggle.1e (from rev 5126, trunk/packages/embassy-domsearch/trunk/debian/manpages/seqfraggle.1e)
===================================================================
--- trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqfraggle.1e (rev 0)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqfraggle.1e 2010-08-11 11:38:04 UTC (rev 5127)
@@ -0,0 +1,78 @@
+'\" t
+.\" Title: SEQFRAGGLE
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 08/11/2010
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: DOMSEARCH 0.1.0++20100721
+.\" Language: English
+.\"
+.TH "SEQFRAGGLE" "1e" "08/11/2010" "DOMSEARCH 0.1.0++20100721" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqfraggle \- Removes fragment sequences from DHF files\&.
+.SH "SYNOPSIS"
+.HP \w'\fBseqfraggle\fR\ 'u
+\fBseqfraggle\fR \fB\-dhfinpath\ \fR\fB\fIdirlist\fR\fR \fB\-thresh\ \fR\fB\fIinteger\fR\fR \fB\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR
+.HP \w'\fBseqfraggle\fR\ 'u
+\fBseqfraggle\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqfraggle\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\-dhfinpath\fR \fIdirlist\fR
+.RS 4
+This option specifies the location of DHF files (domain hits files) or other sequence files (input)\&. A \*(Aqdomain hits file\*(Aq 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\&. Alternatively, SEQFRAGGLE will accept sequence or sequence sets in any of the common formats\&. Default value: \&./
+.RE
+.SS "Required section"
+.PP
+\fB\-thresh\fR \fIinteger\fR
+.RS 4
+This option specifies the percentage of median length for definition of fragments\&. SEQFRAGGLE first determines the median length of all the sequences in the input file, then discards any hit sequences which are not within a threshold percentage of the median length\&. The remaining sequences are written to the output file\&. Default value: 50
+.RE
+.SS "Output section"
+.PP
+\fB\-dhfoutdir\fR \fIoutdir\fR
+.RS 4
+This option specifies the location of DHF files (domain hits files) (output)\&. A \*(Aqdomain hits file\*(Aq 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\&. Alternatively, SEQFRAGGLE will write output files in any of the common formats\&. Default value: \&./
+.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
+seqfraggle is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.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
Deleted: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqnr.1e
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqnr.1e 2010-08-10 14:18:14 UTC (rev 5121)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqnr.1e 2010-08-11 11:38:04 UTC (rev 5127)
@@ -1,144 +0,0 @@
-'\" t
-.\" Title: SEQNR
-.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
-.\" Date: 06/26/2010
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0++20100115
-.\" Language: English
-.\"
-.TH "SEQNR" "1e" "06/26/2010" "EMBOSS 0.1.0++20100115" "EMBOSS Manual for Debian"
-.\" -----------------------------------------------------------------
-.\" * Define some portability stuff
-.\" -----------------------------------------------------------------
-.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.\" http://bugs.debian.org/507673
-.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
-.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.ie \n(.g .ds Aq \(aq
-.el .ds Aq '
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
-.SH "NAME"
-seqnr \- Removes redundancy from DHF files\&.
-.SH "SYNOPSIS"
-.HP \w'\fBseqnr\fR\ 'u
-\fBseqnr\fR \fB\-dhfinpath\ \fR\fB\fIdirlist\fR\fR \fB\-dosing\ \fR\fB\fItoggle\fR\fR \fB\-singletsdir\ \fR\fB\fIdirectory\fR\fR \fB\-dosets\ \fR\fB\fItoggle\fR\fR \fB\-insetsdir\ \fR\fB\fIdirectory\fR\fR [\fB\-matrix\ \fR\fB\fImatrixf\fR\fR] \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-thresh\ \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\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-dored\ \fR\fB\fItoggle\fR\fR \fB\-redoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
-.HP \w'\fBseqnr\fR\ 'u
-\fBseqnr\fR \fB\-help\fR
-.SH "DESCRIPTION"
-.PP
-\fBseqnr\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\-dhfinpath\fR \fIdirlist\fR
-.RS 4
-This option specifies the location of DHF files (domain hits files) (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
-.RE
-.PP
-\fB\-dosing\fR \fItoggle\fR
-.RS 4
-This option specifies whether to use singlet sequences (e\&.g\&. DHF files) to filter input\&. Optionally, up to two further directories of sequences may be read: these are considered in the redundancy calculation but never appear in the output files\&. Default value: Y
-.RE
-.PP
-\fB\-singletsdir\fR \fIdirectory\fR
-.RS 4
-This option specifies the location of singlet filter sequences (e\&.g\&. DHF files) (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
-.RE
-.PP
-\fB\-dosets\fR \fItoggle\fR
-.RS 4
-This option specifies whether to use sets of sequences (e\&.g\&. DHF files) to filter input\&. Optionally, up to two further directories of sequences may be read: these are considered in the redundancy calculation but never appear in the output files\&. Default value: Y
-.RE
-.PP
-\fB\-insetsdir\fR \fIdirectory\fR
-.RS 4
-This option specifies location of sets of filter sequences (e\&.g\&. DAF files) (input)\&. A \*(Aqdomain alignment file\*(Aq contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./
-.RE
-.PP
-\fB\-matrix\fR \fImatrixf\fR
-.RS 4
-This option specifies the residue substitution matrix that is used for sequence comparison\&. Default value: EBLOSUM62
-.RE
-.SS "Required section"
-.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 set of input sequences 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\-thresh\fR \fIfloat\fR
-.RS 4
-This option specifies the % sequence identity redundancy threshold\&. The % sequence identity redundancy threshold 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 (lower limit)\&. The % sequence identity redundancy threshold 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 (upper limit)\&. The % sequence identity redundancy threshold 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\&. 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\-gapextend\fR \fIfloat\fR
-.RS 4
-This option specifies the gap extension penalty\&. 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\-dhfoutdir\fR \fIoutdir\fR
-.RS 4
-This option specifies the location of DHF files (domain hits files) of non\-redundant sequences (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
-.RE
-.PP
-\fB\-dored\fR \fItoggle\fR
-.RS 4
-This option specifies whether to retain redundant sequences\&. If this option is set a DHF file (domain hits file) of redundant sequences is written\&. Default value: N
-.RE
-.PP
-\fB\-redoutdir\fR \fIoutdir\fR
-.RS 4
-This option specifies the location of DHF files (domain hits files) of redundant sequences (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
-.RE
-.PP
-\fB\-logfile\fR \fIoutfile\fR
-.RS 4
-This option specifies the name of SEQNR log file (output)\&. The log file contains messages about any errors arising while SEQNR ran\&. Default value: seqnr\&.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
-seqnr is fully documented via the
-\fBtfm\fR(1)
-system\&.
-.SH "AUTHOR"
-.PP
-\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.RS 4
-Wrote the script used to autogenerate this manual page\&.
-.RE
-.SH "COPYRIGHT"
-.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
Copied: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqnr.1e (from rev 5126, trunk/packages/embassy-domsearch/trunk/debian/manpages/seqnr.1e)
===================================================================
--- trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqnr.1e (rev 0)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqnr.1e 2010-08-11 11:38:04 UTC (rev 5127)
@@ -0,0 +1,144 @@
+'\" t
+.\" Title: SEQNR
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 08/11/2010
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: DOMSEARCH 0.1.0++20100721
+.\" Language: English
+.\"
+.TH "SEQNR" "1e" "08/11/2010" "DOMSEARCH 0.1.0++20100721" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqnr \- Removes redundancy from DHF files\&.
+.SH "SYNOPSIS"
+.HP \w'\fBseqnr\fR\ 'u
+\fBseqnr\fR \fB\-dhfinpath\ \fR\fB\fIdirlist\fR\fR \fB\-dosing\ \fR\fB\fItoggle\fR\fR \fB\-singletsdir\ \fR\fB\fIdirectory\fR\fR \fB\-dosets\ \fR\fB\fItoggle\fR\fR \fB\-insetsdir\ \fR\fB\fIdirectory\fR\fR [\fB\-matrix\ \fR\fB\fImatrixf\fR\fR] \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-thresh\ \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\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-dored\ \fR\fB\fItoggle\fR\fR \fB\-redoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBseqnr\fR\ 'u
+\fBseqnr\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqnr\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\-dhfinpath\fR \fIdirlist\fR
+.RS 4
+This option specifies the location of DHF files (domain hits files) (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
+.RE
+.PP
+\fB\-dosing\fR \fItoggle\fR
+.RS 4
+This option specifies whether to use singlet sequences (e\&.g\&. DHF files) to filter input\&. Optionally, up to two further directories of sequences may be read: these are considered in the redundancy calculation but never appear in the output files\&. Default value: Y
+.RE
+.PP
+\fB\-singletsdir\fR \fIdirectory\fR
+.RS 4
+This option specifies the location of singlet filter sequences (e\&.g\&. DHF files) (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
+.RE
+.PP
+\fB\-dosets\fR \fItoggle\fR
+.RS 4
+This option specifies whether to use sets of sequences (e\&.g\&. DHF files) to filter input\&. Optionally, up to two further directories of sequences may be read: these are considered in the redundancy calculation but never appear in the output files\&. Default value: Y
+.RE
+.PP
+\fB\-insetsdir\fR \fIdirectory\fR
+.RS 4
+This option specifies location of sets of filter sequences (e\&.g\&. DAF files) (input)\&. A \*(Aqdomain alignment file\*(Aq contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./
+.RE
+.PP
+\fB\-matrix\fR \fImatrixf\fR
+.RS 4
+This option specifies the residue substitution matrix that is used for sequence comparison\&. Default value: EBLOSUM62
+.RE
+.SS "Required section"
+.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 set of input sequences 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\-thresh\fR \fIfloat\fR
+.RS 4
+This option specifies the % sequence identity redundancy threshold\&. The % sequence identity redundancy threshold 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 (lower limit)\&. The % sequence identity redundancy threshold 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 (upper limit)\&. The % sequence identity redundancy threshold 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\&. 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\-gapextend\fR \fIfloat\fR
+.RS 4
+This option specifies the gap extension penalty\&. 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\-dhfoutdir\fR \fIoutdir\fR
+.RS 4
+This option specifies the location of DHF files (domain hits files) of non\-redundant sequences (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
+.RE
+.PP
+\fB\-dored\fR \fItoggle\fR
+.RS 4
+This option specifies whether to retain redundant sequences\&. If this option is set a DHF file (domain hits file) of redundant sequences is written\&. Default value: N
+.RE
+.PP
+\fB\-redoutdir\fR \fIoutdir\fR
+.RS 4
+This option specifies the location of DHF files (domain hits files) of redundant sequences (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
+.RE
+.PP
+\fB\-logfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of SEQNR log file (output)\&. The log file contains messages about any errors arising while SEQNR ran\&. Default value: seqnr\&.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
+seqnr is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.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
Deleted: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqsearch.1e
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsearch.1e 2010-08-10 14:18:14 UTC (rev 5121)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqsearch.1e 2010-08-11 11:38:04 UTC (rev 5127)
@@ -1,103 +0,0 @@
-'\" t
-.\" Title: SEQSEARCH
-.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
-.\" Date: 06/26/2010
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0++20100115
-.\" Language: English
-.\"
-.TH "SEQSEARCH" "1e" "06/26/2010" "EMBOSS 0.1.0++20100115" "EMBOSS Manual for Debian"
-.\" -----------------------------------------------------------------
-.\" * Define some portability stuff
-.\" -----------------------------------------------------------------
-.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.\" http://bugs.debian.org/507673
-.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
-.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.ie \n(.g .ds Aq \(aq
-.el .ds Aq '
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
-.SH "NAME"
-seqsearch \- Generate PSI\-BLAST hits (DHF file) from a DAF file\&.
-.SH "SYNOPSIS"
-.HP \w'\fBseqsearch\fR\ 'u
-\fBseqsearch\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-inseqspath\ \fR\fB\fIdirlist\fR\fR \fB\-database\ \fR\fB\fIstring\fR\fR \fB\-niter\ \fR\fB\fIinteger\fR\fR \fB\-evalue\ \fR\fB\fIfloat\fR\fR \fB\-maxhits\ \fR\fB\fIinteger\fR\fR \fB\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
-.HP \w'\fBseqsearch\fR\ 'u
-\fBseqsearch\fR \fB\-help\fR
-.SH "DESCRIPTION"
-.PP
-\fBseqsearch\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\-mode\fR \fIlist\fR
-.RS 4
-This option specifies the mode of SEQSEARCH operation\&. SEQSEARCH takes as input a directory of either i\&. single sequences, ii\&. set of sequences (unaligned or aligned, but typically aligned sequences within a domain alignment file))\&. The user has to specify which\&. Default value: 1
-.RE
-.PP
-\fB\-inseqspath\fR \fIdirlist\fR
-.RS 4
-This option specifies the location of sequences, e\&.g\&. DAF files (domain alignment files) (input)\&. SEQSEARCH takes as input a database of either i\&. single sequences, ii\&. sets of unaligned sequences or iii\&. sets of aligned sequences, e\&.g\&. a domain alignment file\&. A \*(Aqdomain alignment file\*(Aq contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./
-.RE
-.PP
-\fB\-database\fR \fIstring\fR
-.RS 4
-Default value: swissprot
-.RE
-.SS "Required section"
-.PP
-\fB\-niter\fR \fIinteger\fR
-.RS 4
-This option specifies the number of PSIBLAST iterations\&. This option specifies the number of PSIBLAST iterations that are performed in a search\&. Default value: 1
-.RE
-.PP
-\fB\-evalue\fR \fIfloat\fR
-.RS 4
-This option specifies the threshold E\-value for inclusion in family\&. This option specifies the threshold E\-value for a PSIBLAST hit to be retained\&. Default value: 0\&.001
-.RE
-.PP
-\fB\-maxhits\fR \fIinteger\fR
-.RS 4
-This option specifies the maximum number of hits\&. This option specifies the maximum number of PSIBLAST hit that are retained\&. It should normally be set high so that nothing is discarded\&. Default value: 1000
-.RE
-.SS "Output section"
-.PP
-\fB\-dhfoutdir\fR \fIoutdir\fR
-.RS 4
-This option specifies the location of DHF files (domain hits files) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in FASTA format\&. 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\&. Default value: \&./
-.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 SEQSEARCH ran\&. Default value: seqsearch\&.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
-seqsearch is fully documented via the
-\fBtfm\fR(1)
-system\&.
-.SH "AUTHOR"
-.PP
-\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.RS 4
-Wrote the script used to autogenerate this manual page\&.
-.RE
-.SH "COPYRIGHT"
-.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
Copied: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqsearch.1e (from rev 5126, trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsearch.1e)
===================================================================
--- trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqsearch.1e (rev 0)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqsearch.1e 2010-08-11 11:38:04 UTC (rev 5127)
@@ -0,0 +1,103 @@
+'\" t
+.\" Title: SEQSEARCH
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 08/11/2010
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: DOMSEARCH 0.1.0++20100721
+.\" Language: English
+.\"
+.TH "SEQSEARCH" "1e" "08/11/2010" "DOMSEARCH 0.1.0++20100721" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqsearch \- Generate PSI\-BLAST hits (DHF file) from a DAF file\&.
+.SH "SYNOPSIS"
+.HP \w'\fBseqsearch\fR\ 'u
+\fBseqsearch\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-inseqspath\ \fR\fB\fIdirlist\fR\fR \fB\-database\ \fR\fB\fIstring\fR\fR \fB\-niter\ \fR\fB\fIinteger\fR\fR \fB\-evalue\ \fR\fB\fIfloat\fR\fR \fB\-maxhits\ \fR\fB\fIinteger\fR\fR \fB\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBseqsearch\fR\ 'u
+\fBseqsearch\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqsearch\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\-mode\fR \fIlist\fR
+.RS 4
+This option specifies the mode of SEQSEARCH operation\&. SEQSEARCH takes as input a directory of either i\&. single sequences, ii\&. set of sequences (unaligned or aligned, but typically aligned sequences within a domain alignment file))\&. The user has to specify which\&. Default value: 1
+.RE
+.PP
+\fB\-inseqspath\fR \fIdirlist\fR
+.RS 4
+This option specifies the location of sequences, e\&.g\&. DAF files (domain alignment files) (input)\&. SEQSEARCH takes as input a database of either i\&. single sequences, ii\&. sets of unaligned sequences or iii\&. sets of aligned sequences, e\&.g\&. a domain alignment file\&. A \*(Aqdomain alignment file\*(Aq contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./
+.RE
+.PP
+\fB\-database\fR \fIstring\fR
+.RS 4
+Default value: swissprot
+.RE
+.SS "Required section"
+.PP
+\fB\-niter\fR \fIinteger\fR
+.RS 4
+This option specifies the number of PSIBLAST iterations\&. This option specifies the number of PSIBLAST iterations that are performed in a search\&. Default value: 1
+.RE
+.PP
+\fB\-evalue\fR \fIfloat\fR
+.RS 4
+This option specifies the threshold E\-value for inclusion in family\&. This option specifies the threshold E\-value for a PSIBLAST hit to be retained\&. Default value: 0\&.001
+.RE
+.PP
+\fB\-maxhits\fR \fIinteger\fR
+.RS 4
+This option specifies the maximum number of hits\&. This option specifies the maximum number of PSIBLAST hit that are retained\&. It should normally be set high so that nothing is discarded\&. Default value: 1000
+.RE
+.SS "Output section"
+.PP
+\fB\-dhfoutdir\fR \fIoutdir\fR
+.RS 4
+This option specifies the location of DHF files (domain hits files) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in FASTA format\&. 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\&. Default value: \&./
+.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 SEQSEARCH ran\&. Default value: seqsearch\&.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
+seqsearch is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.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
Deleted: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqsort.1e
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsort.1e 2010-08-10 14:18:14 UTC (rev 5121)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqsort.1e 2010-08-11 11:38:04 UTC (rev 5127)
@@ -1,98 +0,0 @@
-'\" t
-.\" Title: SEQSORT
-.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
-.\" Date: 06/26/2010
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0++20100115
-.\" Language: English
-.\"
-.TH "SEQSORT" "1e" "06/26/2010" "EMBOSS 0.1.0++20100115" "EMBOSS Manual for Debian"
-.\" -----------------------------------------------------------------
-.\" * Define some portability stuff
-.\" -----------------------------------------------------------------
-.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.\" http://bugs.debian.org/507673
-.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
-.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.ie \n(.g .ds Aq \(aq
-.el .ds Aq '
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
-.SH "NAME"
-seqsort \- Remove ambiguous classified sequences from DHF files\&.
-.SH "SYNOPSIS"
-.HP \w'\fBseqsort\fR\ 'u
-\fBseqsort\fR \fB\-dhfindir\ \fR\fB\fIdirectory\fR\fR \fB\-overlap\ \fR\fB\fIinteger\fR\fR \fB\-dofamilies\ \fR\fB\fItoggle\fR\fR \fB\-doambiguities\ \fR\fB\fItoggle\fR\fR \fB\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-hitsfile\ \fR\fB\fIoutfile\fR\fR \fB\-ambigfile\ \fR\fB\fIoutfile\fR\fR
-.HP \w'\fBseqsort\fR\ 'u
-\fBseqsort\fR \fB\-help\fR
-.SH "DESCRIPTION"
-.PP
-\fBseqsort\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\-dhfindir\fR \fIdirectory\fR
-.RS 4
-This option specifies the location of DHF files (domain hits files) (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
-.RE
-.SS "Required section"
-.PP
-\fB\-overlap\fR \fIinteger\fR
-.RS 4
-This option specifies the number of overlapping residues required for merging of two hits\&. Each family is also processed so that ovlerapping hits (hits with identical accesssion number that overlap by at least a user\-defined number of residues) are replaced by a hit that is produced from merging the two overlapping hits\&. Default value: 10
-.RE
-.PP
-\fB\-dofamilies\fR \fItoggle\fR
-.RS 4
-This option specifies to write a domain families file\&. If this option is set a domain families file is written\&. Default value: N
-.RE
-.PP
-\fB\-doambiguities\fR \fItoggle\fR
-.RS 4
-This option specifies whether to write a domain ambiguities file\&. If this option is set a domain ambiguities file is written\&. Default value: N
-.RE
-.SS "Output section"
-.PP
-\fB\-dhfoutdir\fR \fIoutdir\fR
-.RS 4
-This option specifies the location of DHF files (domain hits files) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
-.RE
-.PP
-\fB\-hitsfile\fR \fIoutfile\fR
-.RS 4
-This option specifies the name of domain families file (output)\&. A \*(Aqdomain families file\*(Aq contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e\&.g\&. by using SEQSEARCH (psiblast)\&. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included\&. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a \*(Aqdomain ambiguities file\*(Aq\&. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file)\&. Default value: fam\&.dhf
-.RE
-.PP
-\fB\-ambigfile\fR \fIoutfile\fR
-.RS 4
-This option specifies the name of domain ambiguities file (output)\&. A \*(Aqdomain families file\*(Aq contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e\&.g\&. by using SEQSEARCH (psiblast)\&. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included\&. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a \*(Aqdomain ambiguities file\*(Aq\&. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file)\&. Default value: oth\&.dhf
-.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
-seqsort is fully documented via the
-\fBtfm\fR(1)
-system\&.
-.SH "AUTHOR"
-.PP
-\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.RS 4
-Wrote the script used to autogenerate this manual page\&.
-.RE
-.SH "COPYRIGHT"
-.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
Copied: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqsort.1e (from rev 5126, trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsort.1e)
===================================================================
--- trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqsort.1e (rev 0)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqsort.1e 2010-08-11 11:38:04 UTC (rev 5127)
@@ -0,0 +1,98 @@
+'\" t
+.\" Title: SEQSORT
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 08/11/2010
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: DOMSEARCH 0.1.0++20100721
+.\" Language: English
+.\"
+.TH "SEQSORT" "1e" "08/11/2010" "DOMSEARCH 0.1.0++20100721" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqsort \- Remove ambiguous classified sequences from DHF files\&.
+.SH "SYNOPSIS"
+.HP \w'\fBseqsort\fR\ 'u
+\fBseqsort\fR \fB\-dhfindir\ \fR\fB\fIdirectory\fR\fR \fB\-overlap\ \fR\fB\fIinteger\fR\fR \fB\-dofamilies\ \fR\fB\fItoggle\fR\fR \fB\-doambiguities\ \fR\fB\fItoggle\fR\fR \fB\-dhfoutdir\ \fR\fB\fIoutdir\fR\fR \fB\-hitsfile\ \fR\fB\fIoutfile\fR\fR \fB\-ambigfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBseqsort\fR\ 'u
+\fBseqsort\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqsort\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\-dhfindir\fR \fIdirectory\fR
+.RS 4
+This option specifies the location of DHF files (domain hits files) (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
+.RE
+.SS "Required section"
+.PP
+\fB\-overlap\fR \fIinteger\fR
+.RS 4
+This option specifies the number of overlapping residues required for merging of two hits\&. Each family is also processed so that ovlerapping hits (hits with identical accesssion number that overlap by at least a user\-defined number of residues) are replaced by a hit that is produced from merging the two overlapping hits\&. Default value: 10
+.RE
+.PP
+\fB\-dofamilies\fR \fItoggle\fR
+.RS 4
+This option specifies to write a domain families file\&. If this option is set a domain families file is written\&. Default value: N
+.RE
+.PP
+\fB\-doambiguities\fR \fItoggle\fR
+.RS 4
+This option specifies whether to write a domain ambiguities file\&. If this option is set a domain ambiguities file is written\&. Default value: N
+.RE
+.SS "Output section"
+.PP
+\fB\-dhfoutdir\fR \fIoutdir\fR
+.RS 4
+This option specifies the location of DHF files (domain hits files) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
+.RE
+.PP
+\fB\-hitsfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of domain families file (output)\&. A \*(Aqdomain families file\*(Aq contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e\&.g\&. by using SEQSEARCH (psiblast)\&. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included\&. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a \*(Aqdomain ambiguities file\*(Aq\&. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file)\&. Default value: fam\&.dhf
+.RE
+.PP
+\fB\-ambigfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of domain ambiguities file (output)\&. A \*(Aqdomain families file\*(Aq contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e\&.g\&. by using SEQSEARCH (psiblast)\&. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included\&. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a \*(Aqdomain ambiguities file\*(Aq\&. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file)\&. Default value: oth\&.dhf
+.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
+seqsort is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.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
Deleted: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqwords.1e
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqwords.1e 2010-08-10 14:18:14 UTC (rev 5121)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqwords.1e 2010-08-11 11:38:04 UTC (rev 5127)
@@ -1,77 +0,0 @@
-'\" t
-.\" Title: SEQWORDS
-.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
-.\" Date: 06/26/2010
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0++20100115
-.\" Language: English
-.\"
-.TH "SEQWORDS" "1e" "06/26/2010" "EMBOSS 0.1.0++20100115" "EMBOSS Manual for Debian"
-.\" -----------------------------------------------------------------
-.\" * Define some portability stuff
-.\" -----------------------------------------------------------------
-.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.\" http://bugs.debian.org/507673
-.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
-.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-.ie \n(.g .ds Aq \(aq
-.el .ds Aq '
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
-.SH "NAME"
-seqwords \- Generates DHF files from keyword search of UniProt\&.
-.SH "SYNOPSIS"
-.HP \w'\fBseqwords\fR\ 'u
-\fBseqwords\fR \fB\-keyfile\ \fR\fB\fIinfile\fR\fR \fB\-spfile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP \w'\fBseqwords\fR\ 'u
-\fBseqwords\fR \fB\-help\fR
-.SH "DESCRIPTION"
-.PP
-\fBseqwords\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\-keyfile\fR \fIinfile\fR
-.RS 4
-This option specifies the name of keywords file (input)\&. This contains a list of keywords specific to a number of SCOP or CATH families and superfamilies used by SEQWORDS to search a sequence database\&.
-.RE
-.PP
-\fB\-spfile\fR \fIinfile\fR
-.RS 4
-This option specifies the name of the sequence database (input) to search\&.
-.RE
-.SS "Output section"
-.PP
-\fB\-outfile\fR \fIoutfile\fR
-.RS 4
-This option specifies the name of the DHF file (domain hits file) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA\-like)\&. The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH, hits retrieved by a sparse protein signatare by using SIGSCAN or various types of HMM and profile by using LIBSCAN\&. Default value: test\&.hits
-.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
-seqwords is fully documented via the
-\fBtfm\fR(1)
-system\&.
-.SH "AUTHOR"
-.PP
-\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
-.RS 4
-Wrote the script used to autogenerate this manual page\&.
-.RE
-.SH "COPYRIGHT"
-.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
Copied: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqwords.1e (from rev 5126, trunk/packages/embassy-domsearch/trunk/debian/manpages/seqwords.1e)
===================================================================
--- trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqwords.1e (rev 0)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/manpages/seqwords.1e 2010-08-11 11:38:04 UTC (rev 5127)
@@ -0,0 +1,77 @@
+'\" t
+.\" Title: SEQWORDS
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 08/11/2010
+.\" Manual: EMBOSS Manual for Debian
+.\" Source: DOMSEARCH 0.1.0++20100721
+.\" Language: English
+.\"
+.TH "SEQWORDS" "1e" "08/11/2010" "DOMSEARCH 0.1.0++20100721" "EMBOSS Manual for Debian"
+.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
+.\" * set default formatting
+.\" -----------------------------------------------------------------
+.\" disable hyphenation
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+seqwords \- Generates DHF files from keyword search of UniProt\&.
+.SH "SYNOPSIS"
+.HP \w'\fBseqwords\fR\ 'u
+\fBseqwords\fR \fB\-keyfile\ \fR\fB\fIinfile\fR\fR \fB\-spfile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBseqwords\fR\ 'u
+\fBseqwords\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBseqwords\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\-keyfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of keywords file (input)\&. This contains a list of keywords specific to a number of SCOP or CATH families and superfamilies used by SEQWORDS to search a sequence database\&.
+.RE
+.PP
+\fB\-spfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of the sequence database (input) to search\&.
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the name of the DHF file (domain hits file) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA\-like)\&. The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH, hits retrieved by a sparse protein signatare by using SIGSCAN or various types of HMM and profile by using LIBSCAN\&. Default value: test\&.hits
+.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
+seqwords is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+.RS 4
+Wrote the script used to autogenerate this manual page\&.
+.RE
+.SH "COPYRIGHT"
+.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
Deleted: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/rules
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/rules 2010-08-10 14:18:14 UTC (rev 5121)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/rules 2010-08-11 11:38:04 UTC (rev 5127)
@@ -1,6 +0,0 @@
-#!/usr/bin/make -f
-
-include /usr/share/cdbs/1/rules/debhelper.mk
-include /usr/share/cdbs/1/class/autotools.mk
-
-CFLAGS += -I/usr/include/eplplot -I/usr/include/ajax -I/usr/include/nucleus
Copied: trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/rules (from rev 5126, trunk/packages/embassy-domsearch/trunk/debian/rules)
===================================================================
--- trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/rules (rev 0)
+++ trunk/packages/embassy-domsearch/tags/0.1.0++20100721-1/debian/rules 2010-08-11 11:38:04 UTC (rev 5127)
@@ -0,0 +1,9 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/autotools.mk
+
+DEB_CONFIGURE_EXTRA_FLAGS = --enable-systemlibs
+
+CFLAGS += -I/usr/include/eplplot -I/usr/include/ajax -I/usr/include/ajax/epcre -I/usr/include/nucleus
+LDFLAGS += -Wl,--as-needed
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