[med-svn] r21090 - in trunk/packages/exonerate/trunk/debian: . manpages patches

[Andreas Tille]

Author: tille
Date: 2016-01-11 10:55:08 +0000 (Mon, 11 Jan 2016)
New Revision: 21090

Added:
   trunk/packages/exonerate/trunk/debian/manpages/esd2esi.1
Modified:
   trunk/packages/exonerate/trunk/debian/changelog
   trunk/packages/exonerate/trunk/debian/exonerate.manpages
   trunk/packages/exonerate/trunk/debian/patches/manpagesyntax.patch
Log:
fix spelling and manpage syntax issues, add missing manpage, upload to unstable


Modified: trunk/packages/exonerate/trunk/debian/changelog
===================================================================
--- trunk/packages/exonerate/trunk/debian/changelog	2016-01-11 10:54:18 UTC (rev 21089)
+++ trunk/packages/exonerate/trunk/debian/changelog	2016-01-11 10:55:08 UTC (rev 21090)
@@ -1,4 +1,4 @@
-exonerate (2.2.0-7) UNRELEASED; urgency=low
+exonerate (2.2.0-7) unstable; urgency=low
 
   [ Charles Plessy ]
   * renamed debian/upstream-metadata.yaml to debian/upstream/metadata
@@ -19,7 +19,7 @@
   * fix spelling and manpage syntax issues
   * remove outdated README.Debian
 
- -- Andreas Tille <tille at debian.org>  Fri, 09 May 2014 13:17:32 +0200
+ -- Andreas Tille <tille at debian.org>  Mon, 11 Jan 2016 09:54:39 +0100
 
 exonerate (2.2.0-6) unstable; urgency=low
 

Modified: trunk/packages/exonerate/trunk/debian/exonerate.manpages
===================================================================
--- trunk/packages/exonerate/trunk/debian/exonerate.manpages	2016-01-11 10:54:18 UTC (rev 21089)
+++ trunk/packages/exonerate/trunk/debian/exonerate.manpages	2016-01-11 10:55:08 UTC (rev 21090)
@@ -1,2 +1,2 @@
 doc/man/man1/*.1
-debian/manpages/fastaoverlap.1
+debian/manpages/*.1

Added: trunk/packages/exonerate/trunk/debian/manpages/esd2esi.1
===================================================================
--- trunk/packages/exonerate/trunk/debian/manpages/esd2esi.1	                        (rev 0)
+++ trunk/packages/exonerate/trunk/debian/manpages/esd2esi.1	2016-01-11 10:55:08 UTC (rev 21090)
@@ -0,0 +1,14 @@
+.TH ESD2ESI "1" "January 2016" "esd2esi 2.2.0" "User Commands"
+.SH NAME
+esd2esi \- generate an exonerate sequence index file
+.SH SYNOPSIS:
+esd2esi <path> <path>
+.SH DESCRIPTION
+esd2esi from exonerate version 2.2.0
+.PP
+esd2esi: generate an exonerate sequence index file
+.PP
+.SH AUTHOR
+The author of this software is Guy St.C. Slater. guy at ebi.ac.uk. 2007.
+.P
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

Modified: trunk/packages/exonerate/trunk/debian/patches/manpagesyntax.patch
===================================================================
--- trunk/packages/exonerate/trunk/debian/patches/manpagesyntax.patch	2016-01-11 10:54:18 UTC (rev 21089)
+++ trunk/packages/exonerate/trunk/debian/patches/manpagesyntax.patch	2016-01-11 10:55:08 UTC (rev 21090)
@@ -13,6 +13,42 @@
  Some of the command line options for the exonerate-server are the same as for the
  exonerate client, and these are documented in the man page for
  .B exonerate.
+@@ -130,7 +130,7 @@ are reported by the server about what is
+ 
+ .RE
+ .SH INTERFACE
+-.T
++.TP
+ This section documents the communication interface between
+ the client and server.
+ The interface is documented for people wishing to write their own
+@@ -369,7 +369,7 @@ reply line.
+ .P
+ .PP
+ .nf
+-.SP
++.sp
+ 
+ % telnet localhost 12886
+ Trying 127.0.0.1...
+@@ -416,7 +416,7 @@ hspset: 25849 15 445 22
+ hspset: 93938 26 265 34
+ % exit
+ Connection closed by foreign host.
+-.SP
++.sp
+ .fi
+ 
+ .\"
+@@ -445,7 +445,7 @@ This documentation accompanies version 2
+ .\"
+ .SH AUTHOR
+ Guy St.C. Slater.  <guy at ebi.ac.uk>.
+-.L
++.P
+ See the AUTHORS file accompanying the source code
+ for a list of contributors.
+ .SH AVAILABILITY
 --- a/doc/man/man1/exonerate.1
 +++ b/doc/man/man1/exonerate.1
 @@ -45,13 +45,13 @@ rather than on the symbols.
@@ -31,6 +67,15 @@
  .fi
  .\"
  Hence the subsequence "CG" would have start=1,
+@@ -86,7 +86,7 @@ and the gap penalties.
+ 
+ .RE
+ .SH GENERAL OPTIONS
+-.T
++.TP
+ Most arguments have short and long forms.  The long forms
+ are more likely to be stable over time, and hence should
+ be used in scripts which call exonerate.
 @@ -1194,7 +1194,7 @@ show the observed relative frequencies o
  the splice sites in the chosen organism (in ACGT order).
  
@@ -63,6 +108,15 @@
  .fi
  
  .TP
+@@ -1338,7 +1338,7 @@ This documentation accompanies version 2
+ .\"
+ .SH AUTHOR
+ Guy St.C. Slater.  <guy at ebi.ac.uk>.
+-.L
++.P
+ See the AUTHORS file accompanying the source code
+ for a list of contributors.
+ .SH AVAILABILITY
 --- a/doc/man/man1/fastautils.1
 +++ b/doc/man/man1/fastautils.1
 @@ -72,7 +72,7 @@ This documentation accompanies version 2
@@ -76,7 +130,7 @@
  .SH AVAILABILITY
 --- a/doc/man/man1/ipcress.1
 +++ b/doc/man/man1/ipcress.1
-@@ -67,11 +67,11 @@ Maximum product length to report
+@@ -67,16 +67,16 @@ Maximum product length to report
  .RE
  .P
  Here is an example line in this format:
@@ -90,3 +144,27 @@
  .fi
  .\"
  .RE
+ .SH OUTPUT FORMAT
+-.T
++.TP
+ The output format describes one PCR product per-line,
+ and is prefixed by "ipcress:", followed by the following 11 fields:
+ .\"
+@@ -159,7 +159,7 @@ is not designed for parsing (see: --pret
+ .\"
+ .RE
+ .SH GENERAL OPTIONS
+-.T
++.TP
+ Most arguments have short and long forms.  The long forms
+ are more likely to be stable over time, and hence should
+ be used in scripts which call ipcress.
+@@ -257,7 +257,7 @@ This documentation accompanies version 2
+ .\"
+ .SH AUTHOR
+ Guy St.C. Slater.  <guy at ebi.ac.uk>.
+-.L
++.P
+ See the AUTHORS file accompanying the source code
+ for a list of contributors.
+ .SH AVAILABILITY