[med-svn] r8179 - trunk/packages/gmod/gbrowse/trunk/debian

[olivier sallou]

Author: osallou-guest
Date: 2011-10-18 17:13:32 +0000 (Tue, 18 Oct 2011)
New Revision: 8179

Added:
   trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignment_database.1
   trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignments_msa.1
Removed:
   trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignement_database.1
   trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignements_msa.1
Modified:
   trunk/packages/gmod/gbrowse/trunk/debian/lintian-overrides
Log:
fix manpage name, add override

Deleted: trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignement_database.1
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignement_database.1	2011-10-18 17:10:55 UTC (rev 8178)
+++ trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignement_database.1	2011-10-18 17:13:32 UTC (rev 8179)
@@ -1,13 +0,0 @@
-.TH GBrowse2 1  "October 18, 2011" "version 1.1.0" "USER COMMANDS"
-
-.SH NAME
-gbrowse_syn_load_alignment_database \- Script to load the database for gbrowse_syn
-.SH DESCRIPTION
- The expected file format is tab-delimited (shown below):
- species1  ref1  start1 end1 strand1  cigar_string1 species2  ref2  start2 end2 strand2  cigar_string2 coords1... | coords2...
- the coordinate format: pos1_species1 pos1_species2 ... posn_species1 posn_species2 | pos1_species2 pos1_species1 ... posn_species2 posn_species1,
- where pos is the matching sequence coordinate (ungapped) in each species.
-.PP
-.SH AUTHOR
-Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
-Lincoln Stein - GBrowse

Deleted: trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignements_msa.1
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignements_msa.1	2011-10-18 17:10:55 UTC (rev 8178)
+++ trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignements_msa.1	2011-10-18 17:13:32 UTC (rev 8179)
@@ -1,11 +0,0 @@
-.TH GBrowse2 1  "October 18, 2011" "version 1.1.0" "USER COMMANDS"
-
-.SH NAME
-gbrowse_syn_load_alignments_msa \- Script to load the database for gbrowse_syn from alignement file
-.SH DESCRIPTION
- This script will load the gbrowse_syn alignment database directly from a
- multiple sequence alignment file.
-.PP
-.SH AUTHOR
-Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
-Lincoln Stein - GBrowse

Copied: trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignment_database.1 (from rev 8176, trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignement_database.1)
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignment_database.1	                        (rev 0)
+++ trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignment_database.1	2011-10-18 17:13:32 UTC (rev 8179)
@@ -0,0 +1,13 @@
+.TH GBrowse2 1  "October 18, 2011" "version 1.1.0" "USER COMMANDS"
+
+.SH NAME
+gbrowse_syn_load_alignment_database \- Script to load the database for gbrowse_syn
+.SH DESCRIPTION
+ The expected file format is tab-delimited (shown below):
+ species1  ref1  start1 end1 strand1  cigar_string1 species2  ref2  start2 end2 strand2  cigar_string2 coords1... | coords2...
+ the coordinate format: pos1_species1 pos1_species2 ... posn_species1 posn_species2 | pos1_species2 pos1_species1 ... posn_species2 posn_species1,
+ where pos is the matching sequence coordinate (ungapped) in each species.
+.PP
+.SH AUTHOR
+Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
+Lincoln Stein - GBrowse

Copied: trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignments_msa.1 (from rev 8176, trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignements_msa.1)
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignments_msa.1	                        (rev 0)
+++ trunk/packages/gmod/gbrowse/trunk/debian/gbrowse_syn_load_alignments_msa.1	2011-10-18 17:13:32 UTC (rev 8179)
@@ -0,0 +1,11 @@
+.TH GBrowse2 1  "October 18, 2011" "version 1.1.0" "USER COMMANDS"
+
+.SH NAME
+gbrowse_syn_load_alignments_msa \- Script to load the database for gbrowse_syn from alignement file
+.SH DESCRIPTION
+ This script will load the gbrowse_syn alignment database directly from a
+ multiple sequence alignment file.
+.PP
+.SH AUTHOR
+Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
+Lincoln Stein - GBrowse

Modified: trunk/packages/gmod/gbrowse/trunk/debian/lintian-overrides
===================================================================
--- trunk/packages/gmod/gbrowse/trunk/debian/lintian-overrides	2011-10-18 17:10:55 UTC (rev 8178)
+++ trunk/packages/gmod/gbrowse/trunk/debian/lintian-overrides	2011-10-18 17:13:32 UTC (rev 8179)
@@ -1 +1,2 @@
 gbrowse: manpage-has-errors-from-man usr/share/man/man3/Bio::Graphics::Browser2::PluginSet.3pm.gz 139: warning [p 1, 1.8i, div `an-div', 0.2i]: can't break line
+gbrowse: script-not-executable etc/gbrowse/MobyServices/GbrowseServices.pm