[med-svn] r6423 - in trunk/packages/gbrowse/trunk/debian: . patches
olivier sallou
osallou-guest at alioth.debian.org
Fri Apr 1 12:12:45 UTC 2011
Author: osallou-guest
Date: 2011-04-01 12:12:40 +0000 (Fri, 01 Apr 2011)
New Revision: 6423
Added:
trunk/packages/gbrowse/trunk/debian/gbrowse.1
trunk/packages/gbrowse/trunk/debian/gbrowse_change_passwd.1
trunk/packages/gbrowse/trunk/debian/gbrowse_create_account.1
trunk/packages/gbrowse/trunk/debian/gbrowse_metadb_config.1
trunk/packages/gbrowse/trunk/debian/gbrowse_set_admin_passwd.1
trunk/packages/gbrowse/trunk/debian/gbrowse_slave.1
trunk/packages/gbrowse/trunk/debian/scan_gbrowse.1
Modified:
trunk/packages/gbrowse/trunk/debian/gbrowse.manpages
trunk/packages/gbrowse/trunk/debian/patches/debian-packaging-patch
Log:
add new man pages in debian dir and remove them from patch
Added: trunk/packages/gbrowse/trunk/debian/gbrowse.1
===================================================================
--- trunk/packages/gbrowse/trunk/debian/gbrowse.1 (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/gbrowse.1 2011-04-01 12:12:40 UTC (rev 6423)
@@ -0,0 +1,45 @@
+.TH GBrowse2 1 "February 07, 2011" "version 1.1.0" "USER COMMANDS"
+.SH NAME
+GBrowse2 \- The Generic Genome Browser
+.SH SYNOPSIS
+.B libgbrowse-perl
+[\-h]
+.SH INSTALLATION
+If Apache2 is installed on the system, the software has configured it to link URLs to GBrowse directories. A restart of Apache is required to take it into account. Configuration is available in /etc/gbrowse2/apache2.conf file.
+ If an other web server is used, one should refer to the apache2 template to map urls in the same way.
+.PP
+.SH DEPENDENCIES
+Additional optional perl dependencies exist to provide additional features. Please refer to Optional modules in INSTALL file for more information.
+.PP
+.SH CONFIGURATION
+.B gbrowse2
+Configuration files are located in /etc/gbrowse. Main configuration file is GBrowse.conf. It contains the global configuration elements. Specific configuration files are located in the same directory per data bank. For more details, one should refer to the GBrowse documentation.
+ Installation is provided with a Yeast genome sample.
+.PP
+.SH DESCRIPTION
+GBrowse is a simple but highly
+ configurable web-based genome browser. It is a component of the
+ Generic Model Organism Systems Database project (GMOD).
+ Some of its features:
+ * Simultaneous bird's eye and detailed views of the genome;
+ * Scroll, zoom, center;
+ * Attach arbitrary URLs to any annotation;
+ * Order and appearance of tracks are customizable by administrator and
+ end-user;
+ * Search by annotation ID, name, or comment;
+ * Supports third party annotation using GFF formats;
+ * Settings persist across sessions;
+ * DNA and GFF dumps;
+ * Connectivity to different databases, including BioSQL and Chado;
+ * Multi-language support;
+ * Third-party feature loading;
+ * Customizable plug-in architecture (e.g. run BLAST, dump & import many
+ formats, find oligonucleotides, design primers, create restriction maps,
+ edit features).
+.PP
+.SH WEB ACCESS
+GBrowse is accessible at URL http://localhost/gbrowse2
+.PP
+.SH AUTHOR
+Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
+Lincoln Stein - GBrowse
Modified: trunk/packages/gbrowse/trunk/debian/gbrowse.manpages
===================================================================
--- trunk/packages/gbrowse/trunk/debian/gbrowse.manpages 2011-04-01 11:42:40 UTC (rev 6422)
+++ trunk/packages/gbrowse/trunk/debian/gbrowse.manpages 2011-04-01 12:12:40 UTC (rev 6423)
@@ -1,3 +1,3 @@
-docs/*.1
+debian/*.1
debian/gbrowse/man/man1/*
debian/gbrowse/man/man3/*
Added: trunk/packages/gbrowse/trunk/debian/gbrowse_change_passwd.1
===================================================================
--- trunk/packages/gbrowse/trunk/debian/gbrowse_change_passwd.1 (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/gbrowse_change_passwd.1 2011-04-01 12:12:40 UTC (rev 6423)
@@ -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
Added: trunk/packages/gbrowse/trunk/debian/gbrowse_create_account.1
===================================================================
--- trunk/packages/gbrowse/trunk/debian/gbrowse_create_account.1 (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/gbrowse_create_account.1 2011-04-01 12:12:40 UTC (rev 6423)
@@ -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
Added: trunk/packages/gbrowse/trunk/debian/gbrowse_metadb_config.1
===================================================================
--- trunk/packages/gbrowse/trunk/debian/gbrowse_metadb_config.1 (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/gbrowse_metadb_config.1 2011-04-01 12:12:40 UTC (rev 6423)
@@ -0,0 +1,22 @@
+.TH GBrowse2 1 "February 07, 2011" "version 1.1.0" "USER COMMANDS"
+.SH NAME
+gbrowse_metadb_config \- Initializes an empty GBrowse user accounts and uploads metadata database
+.SH SYNOPSIS
+.B gbrowse_metadb_config [-dns password -admin user:pass]
+.I dns Provide a custom DBI connection string, overriding what is
+set in Gbrowse.conf. Note that if there are semicolons in the
+string (like most MySQL connection DSNs will), you WILL have
+to escape it with quotes.
+.I "[-admin user:pass]" Provide an administrator username and password (in the form
+user:pass) to skip the prompts if the database does not
+exist.
+.PP
+.SH DESCRIPTION
+Initializes an empty GBrowse user accounts and uploads metadata database.
+Currently mysql and SQLite databases are supported. When creating a
+mysql database you must provide the -admin option to specify a user
+and password that has database create privileges on the server.
+.PP
+.SH AUTHOR
+Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
+Lincoln Stein - GBrowse
Added: trunk/packages/gbrowse/trunk/debian/gbrowse_set_admin_passwd.1
===================================================================
--- trunk/packages/gbrowse/trunk/debian/gbrowse_set_admin_passwd.1 (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/gbrowse_set_admin_passwd.1 2011-04-01 12:12:40 UTC (rev 6423)
@@ -0,0 +1,23 @@
+.TH GBrowse2 1 "February 07, 2011" "version 1.1.0" "USER COMMANDS"
+.SH NAME
+gbrowse_setadmin_passwd \- Sets the adminstrator password for the GBrowse admin
+.SH SYNOPSIS
+.B gbrowse_create_account [-pass password -name user]
+.I user Admin user name (default, admin)
+.I "[-pass password]" Password is not provided on the command line, you will be prompted for it on standard input
+.PP
+.SH DESCRIPTION
+This script uses the "user_account_db" and "admin_account" options
+in the currently installed GBrowse.conf configuration file to find
+the appropriate accounts database and the name of the administrator.
+If a password is not provided on the command line, you will be
+prompted for it on standard input.
+.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
Added: trunk/packages/gbrowse/trunk/debian/gbrowse_slave.1
===================================================================
--- trunk/packages/gbrowse/trunk/debian/gbrowse_slave.1 (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/gbrowse_slave.1 2011-04-01 12:12:40 UTC (rev 6423)
@@ -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/patches/debian-packaging-patch
===================================================================
--- trunk/packages/gbrowse/trunk/debian/patches/debian-packaging-patch 2011-04-01 11:42:40 UTC (rev 6422)
+++ trunk/packages/gbrowse/trunk/debian/patches/debian-packaging-patch 2011-04-01 12:12:40 UTC (rev 6423)
@@ -1,52 +1,4 @@
Patch to fit debian packaging - Olivier Sallou - February 2011
---- /dev/null
-+++ b/docs/gbrowse.1
-@@ -0,0 +1,45 @@
-+.TH GBrowse2 1 "February 07, 2011" "version 1.1.0" "USER COMMANDS"
-+.SH NAME
-+GBrowse2 \- The Generic Genome Browser
-+.SH SYNOPSIS
-+.B libgbrowse-perl
-+[\-h]
-+.SH INSTALLATION
-+If Apache2 is installed on the system, the software has configured it to link URLs to GBrowse directories. A restart of Apache is required to take it into account. Configuration is available in /etc/gbrowse2/apache2.conf file.
-+ If an other web server is used, one should refer to the apache2 template to map urls in the same way.
-+.PP
-+.SH DEPENDENCIES
-+Additional optional perl dependencies exist to provide additional features. Please refer to Optional modules in INSTALL file for more information.
-+.PP
-+.SH CONFIGURATION
-+.B gbrowse2
-+Configuration files are located in /etc/gbrowse. Main configuration file is GBrowse.conf. It contains the global configuration elements. Specific configuration files are located in the same directory per data bank. For more details, one should refer to the GBrowse documentation.
-+ Installation is provided with a Yeast genome sample.
-+.PP
-+.SH DESCRIPTION
-+GBrowse is a simple but highly
-+ configurable web-based genome browser. It is a component of the
-+ Generic Model Organism Systems Database project (GMOD).
-+ Some of its features:
-+ * Simultaneous bird's eye and detailed views of the genome;
-+ * Scroll, zoom, center;
-+ * Attach arbitrary URLs to any annotation;
-+ * Order and appearance of tracks are customizable by administrator and
-+ end-user;
-+ * Search by annotation ID, name, or comment;
-+ * Supports third party annotation using GFF formats;
-+ * Settings persist across sessions;
-+ * DNA and GFF dumps;
-+ * Connectivity to different databases, including BioSQL and Chado;
-+ * Multi-language support;
-+ * Third-party feature loading;
-+ * Customizable plug-in architecture (e.g. run BLAST, dump & import many
-+ formats, find oligonucleotides, design primers, create restriction maps,
-+ edit features).
-+.PP
-+.SH WEB ACCESS
-+GBrowse is accessible at URL http://localhost/gbrowse2
-+.PP
-+.SH AUTHOR
-+Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
-+Lincoln Stein - GBrowse
--- a/install_util/GBrowseInstall.pm
+++ b/install_util/GBrowseInstall.pm
@@ -403,6 +403,84 @@
@@ -181,155 +133,6 @@
=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
---- /dev/null
-+++ b/docs/scan_gbrowse.1
-@@ -0,0 +1,16 @@
-+.TH GBrowse2 1 "February 07, 2011" "version 1.1.0" "USER COMMANDS"
-+.SH NAME
-+scan_gbrowse \- Scan the gbrowse2 instance for discoverable tracks
-+.SH SYNOPSIS
-+.B scan_gbrowse [ --cache cachetime] URL
-+.I url GBrowse URL to scan
-+.I "[--cache cachetime]" Cache the results in a temporary file for cachetime seconds
-+.PP
-+.SH DESCRIPTION
-+Scan the gbrowse2 instance at <gbrowse_url> for discoverable tracks
-+and create appropriate remote track configuration stanzas suitable for
-+incorporation into the local gbrowse2 config file.
-+.PP
-+.SH AUTHOR
-+Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
-+Lincoln Stein - GBrowse
---- /dev/null
-+++ b/docs/gbrowse_metadb_config.1
-@@ -0,0 +1,22 @@
-+.TH GBrowse2 1 "February 07, 2011" "version 1.1.0" "USER COMMANDS"
-+.SH NAME
-+gbrowse_metadb_config \- Initializes an empty GBrowse user accounts and uploads metadata database
-+.SH SYNOPSIS
-+.B gbrowse_metadb_config [-dns password -admin user:pass]
-+.I dns Provide a custom DBI connection string, overriding what is
-+set in Gbrowse.conf. Note that if there are semicolons in the
-+string (like most MySQL connection DSNs will), you WILL have
-+to escape it with quotes.
-+.I "[-admin user:pass]" Provide an administrator username and password (in the form
-+user:pass) to skip the prompts if the database does not
-+exist.
-+.PP
-+.SH DESCRIPTION
-+Initializes an empty GBrowse user accounts and uploads metadata database.
-+Currently mysql and SQLite databases are supported. When creating a
-+mysql database you must provide the -admin option to specify a user
-+and password that has database create privileges on the server.
-+.PP
-+.SH AUTHOR
-+Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
-+Lincoln Stein - GBrowse
---- /dev/null
-+++ b/docs/gbrowse_set_admin_passwd.1
-@@ -0,0 +1,23 @@
-+.TH GBrowse2 1 "February 07, 2011" "version 1.1.0" "USER COMMANDS"
-+.SH NAME
-+gbrowse_setadmin_passwd \- Sets the adminstrator password for the GBrowse admin
-+.SH SYNOPSIS
-+.B gbrowse_create_account [-pass password -name user]
-+.I user Admin user name (default, admin)
-+.I "[-pass password]" Password is not provided on the command line, you will be prompted for it on standard input
-+.PP
-+.SH DESCRIPTION
-+This script uses the "user_account_db" and "admin_account" options
-+in the currently installed GBrowse.conf configuration file to find
-+the appropriate accounts database and the name of the administrator.
-+If a password is not provided on the command line, you will be
-+prompted for it on standard input.
-+.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
--- a/lib/Bio/DB/GFF/Aggregator/match_gap.pm
+++ b/lib/Bio/DB/GFF/Aggregator/match_gap.pm
@@ -34,7 +34,6 @@
Added: trunk/packages/gbrowse/trunk/debian/scan_gbrowse.1
===================================================================
--- trunk/packages/gbrowse/trunk/debian/scan_gbrowse.1 (rev 0)
+++ trunk/packages/gbrowse/trunk/debian/scan_gbrowse.1 2011-04-01 12:12:40 UTC (rev 6423)
@@ -0,0 +1,16 @@
+.TH GBrowse2 1 "February 07, 2011" "version 1.1.0" "USER COMMANDS"
+.SH NAME
+scan_gbrowse \- Scan the gbrowse2 instance for discoverable tracks
+.SH SYNOPSIS
+.B scan_gbrowse [ --cache cachetime] URL
+.I url GBrowse URL to scan
+.I "[--cache cachetime]" Cache the results in a temporary file for cachetime seconds
+.PP
+.SH DESCRIPTION
+Scan the gbrowse2 instance at <gbrowse_url> for discoverable tracks
+and create appropriate remote track configuration stanzas suitable for
+incorporation into the local gbrowse2 config file.
+.PP
+.SH AUTHOR
+Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging
+Lincoln Stein - GBrowse
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