[med-svn] r6115 - in trunk/packages/gbrowse/trunk/debian: . patches

[olivier sallou]

Author: osallou-guest
Date: 2011-02-28 15:15:09 +0000 (Mon, 28 Feb 2011)
New Revision: 6115

Modified:
   trunk/packages/gbrowse/trunk/debian/gbrowse.manpages
   trunk/packages/gbrowse/trunk/debian/patches/debian-packaging-patch
   trunk/packages/gbrowse/trunk/debian/rules
Log:
add some man pages

Modified: trunk/packages/gbrowse/trunk/debian/gbrowse.manpages
===================================================================
--- trunk/packages/gbrowse/trunk/debian/gbrowse.manpages	2011-02-28 14:23:36 UTC (rev 6114)
+++ trunk/packages/gbrowse/trunk/debian/gbrowse.manpages	2011-02-28 15:15:09 UTC (rev 6115)
@@ -1,3 +1,8 @@
 docs/gbrowse.1
+docs/gbrowse_change_passwd.1
+docs/gbrowse_metadb_config.1
+docs/gbrowse_create_account.1
+docs/gbrowse_slave.1
+docs/scan_gbrowse.1
 debian/gbrowse/man/man1/*
 debian/gbrowse/man/man3/*

Modified: trunk/packages/gbrowse/trunk/debian/patches/debian-packaging-patch
===================================================================
--- trunk/packages/gbrowse/trunk/debian/patches/debian-packaging-patch	2011-02-28 14:23:36 UTC (rev 6114)
+++ trunk/packages/gbrowse/trunk/debian/patches/debian-packaging-patch	2011-02-28 15:15:09 UTC (rev 6115)
@@ -159,3 +159,104 @@
  # Short-Description: Start/Stop the gbrowse_slave rendering server.
  ### END INIT INFO
  
+--- a/bin/gtf2gff3.pl
++++ b/bin/gtf2gff3.pl
+@@ -1320,7 +1320,7 @@
+ 
+ =head1 NAME
+ 
+-gtf2gff3
++gtf2gff3 - Converts GTF formatted files to valid GFF3 files
+ 
+ =head1 VERSION
+ 
+--- a/bin/wiggle2gff3.pl
++++ b/bin/wiggle2gff3.pl
+@@ -2,7 +2,7 @@
+ 
+ =head1 NAME
+ 
+-wiggle2gff3.pl
++wiggle2gff3.pl - Converts UCSC WIG format files into gff3 files
+ 
+ =head1 SYNOPSIS
+ 
+--- /dev/null
++++ b/docs/gbrowse_change_passwd.1
+@@ -0,0 +1,12 @@
++.TH GBrowse2 1  "February 07, 2011" "version 1.1.0" "USER COMMANDS"
++.SH NAME
++gbrowse_change_passwd \- Modify a gbrowse user password
++.SH SYNOPSIS
++.B gbrowse_change_passwd  user [passwd]
++.I user GBrowse user name
++.I [passwd] If no password is provided on the command line, then
++a new random password will be chosen.
++.PP
++.SH AUTHOR
++Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
++Lincoln Stein - GBrowse
+--- /dev/null
++++ b/docs/gbrowse_create_account.1
+@@ -0,0 +1,26 @@
++.TH GBrowse2 1  "February 07, 2011" "version 1.1.0" "USER COMMANDS"
++.SH NAME
++gbrowse_create_account \- Creates an account for GBrowse
++.SH SYNOPSIS
++.B gbrowse_create_account [-pass password -fullname name -email address] user
++.I user GBrowse user name
++.I "[-pass password]" If a password is not provided on the command line, you will be prompted for it on standard input
++.I "[-fullname name]" User full name
++.I "[-email address]" User email
++.PP
++.SH DESCRIPTION
++Creates a user account with the desired username and
++password. If the account already exists, then the password
++is reset.
++This script uses the "user_account_db"  option in the currently
++installed GBrowse.conf configuration file to find
++the appropriate accounts database.
++.br
++.B WARNING:
++This script should be run as the web server user using
++"sudo -u www-data $0". If it detects that it is not being run as this
++user, it will attempt to sudo itself for you.
++.PP
++.SH AUTHOR
++Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
++Lincoln Stein - GBrowse
+--- /dev/null
++++ b/docs/gbrowse_slave.1
+@@ -0,0 +1,32 @@
++.TH GBrowse2 1  "February 07, 2011" "version 1.1.0" "USER COMMANDS"
++.SH NAME
++gbrowse_slave \- Creates an account for GBrowse
++.SH SYNOPSIS
++.B gbrowse_slave [options]
++.I "[-p  portnumber]"  Network port number to listen to (default 8101)
++.I "[-v level]"  Verbosity level (0-3)
++.I "[-u name]" User to run under (same as current)
++.I "[-l path]" Log file path (default, use STDERR)
++.I "[--pid path]" PID file path (default, none)
++.I "[-preload path]" Path to a config file containing override information
++ and databases to preload
++.I "[-T path]" Override location of configuration file cache files.
++.PP
++.SH DESCRIPTION
++Bare-naked Gbrowse render server.  Launch with the port number to
++listen on.
++No other configuration information is necessary. The needed
++configuration will be transmitted from the master server at run
++time.
++If you need to override some configuration information (for example,
++to specify a different tmp_base directory for session information),
++you may place it in a configuration file in the [GENERAL] section. All
++options in the [GENERAL] section will override the transmitted
++information.
++Any [name:database] sections containing database information located
++in the preload config file will be preloaded to reduce execution
++latency.
++.PP
++.SH AUTHOR
++Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
++Lincoln Stein - GBrowse

Modified: trunk/packages/gbrowse/trunk/debian/rules
===================================================================
--- trunk/packages/gbrowse/trunk/debian/rules	2011-02-28 14:23:36 UTC (rev 6114)
+++ trunk/packages/gbrowse/trunk/debian/rules	2011-02-28 15:15:09 UTC (rev 6115)
@@ -23,7 +23,7 @@
 	mv debian/gbrowse/lib/perl5/*/* debian/gbrowse/usr/lib/perl5/
 	rm -rf debian/gbrowse/lib
 	rm -f debian/gbrowse/usr/share/doc/gbrowse/INSTALL
-	rm -f debian/gbrowse/lib/perl5/auto/GBrowse/.packlist
+	rm -f debian/gbrowse/usr/lib/perl5/auto/GBrowse/.packlist
 	chmod 644 debian/gbrowse/etc/gbrowse2/MobyServices/text_xml_renderer.pm
 	chmod 644 debian/gbrowse/etc/gbrowse2/synteny/oryza.synconf.disabled
 	chmod 755 debian/gbrowse/etc/default/gbrowse-slave