mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Update links to reflect Galaxy Wiki moving away from Bitbucket.
This commit is contained in:
Nick Semenkovich
+1
-1
@@ -28,4 +28,4 @@ on adding tools can be found on the Galaxy website (linked above).
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Not all dependencies are included for the tools provided in the sample
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tool_conf.xml. A full list of external dependencies is available at:
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http://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies
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http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
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+1
-1
@@ -3,7 +3,7 @@
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; eggs.g2.bx.psu.edu). Probably only useful to Galaxy developers at
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; Penn State. This file is used by scripts/dist-scramble.py
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;
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; More information: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Eggs
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; More information: http://wiki.g2.bx.psu.edu/Admin/Config/Eggs
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;
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[hosts]
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@@ -3,7 +3,7 @@
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;
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; This file is version controlled and should not be edited by hand!
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; For more information, see:
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; http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Eggs
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; http://wiki.g2.bx.psu.edu/Admin/Config/Eggs
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;
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[general]
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@@ -17,7 +17,7 @@ The 'pbs' runner depends on 'pbs_python' which is not installed or not
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configured properly. Galaxy's "scramble" system should make this installation
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simple, please follow the instructions found at:
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http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
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http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
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Additional errors may follow:
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%s
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@@ -14,7 +14,7 @@ The 'sge' runner depends on 'DRMAA_python' which is not installed. Galaxy's
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"scramble" system should make this installation simple, please follow the
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instructions found at:
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http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
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http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
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Additional errors may follow:
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%s
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@@ -64,7 +64,7 @@ class Configuration( object ):
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self.nginx_upload_path = kwargs.get( 'nginx_upload_path', False )
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self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) )
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self.brand = kwargs.get( 'brand', None )
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self.wiki_url = kwargs.get( 'wiki_url', 'http://bitbucket.org/galaxy/galaxy-central/wiki/Home' )
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self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' )
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self.bugs_email = kwargs.get( 'bugs_email', None )
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self.blog_url = kwargs.get( 'blog_url', None )
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self.screencasts_url = kwargs.get( 'screencasts_url', None )
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@@ -49,7 +49,7 @@ class Configuration( object ):
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self.smtp_server = kwargs.get( 'smtp_server', None )
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self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) )
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self.brand = kwargs.get( 'brand', None )
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self.wiki_url = kwargs.get( 'wiki_url', 'http://bitbucket.org/galaxy/galaxy-central/wiki/Home' )
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self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' )
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self.bugs_email = kwargs.get( 'bugs_email', None )
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self.blog_url = kwargs.get( 'blog_url', None )
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self.screencasts_url = kwargs.get( 'screencasts_url', None )
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@@ -33,7 +33,7 @@ class Configuration( object ):
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self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail")
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self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) )
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self.brand = kwargs.get( 'brand', None )
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self.wiki_url = kwargs.get( 'wiki_url', 'http://bitbucket.org/galaxy/galaxy-central/wiki/Home' )
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self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' )
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self.bugs_email = kwargs.get( 'bugs_email', None )
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self.blog_url = kwargs.get( 'blog_url', None )
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self.screencasts_url = kwargs.get( 'screencasts_url', None )
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+1
-1
@@ -30,7 +30,7 @@ Need Help?
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.. __: /static/help.html
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.. __: http://www.bx.psu.edu/cgi-bin/trac.cgi
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.. __: http://bitbucket.org/galaxy/galaxy-central/wiki/GalaxyTeam
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.. __: http://wiki.g2.bx.psu.edu/Galaxy%20Team
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.. __: mailto:galaxy@bx.psu.edu
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Version: <b>2.1</b> Revision: <b>$Rev$</b>
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@@ -34,9 +34,9 @@
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<div class="submenu">
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<ul>
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<li><a href="${app.config.get( "bugs_email", "mailto:galaxy-bugs@bx.psu.edu" )}">Email comments, bug reports, or suggestions</a></li>
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<li><a target="_blank" href="${app.config.get( "wiki_url", "http://bitbucket.org/galaxy/galaxy-central/wiki" )}">Galaxy Wiki</a></li>
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<li><a target="_blank" href="${app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" )}">Galaxy Wiki</a></li>
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<li><a target="_blank" href="${app.config.get( "screencasts_url", "http://galaxycast.org" )}">Video tutorials (screencasts)</a></li>
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<li><a target="_blank" href="${app.config.get( "citation_url", "http://bitbucket.org/galaxy/galaxy-central/wiki/Citations" )}">How to Cite Galaxy</a></li>
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<li><a target="_blank" href="${app.config.get( "citation_url", "http://wiki.g2.bx.psu.edu/Citing%20Galaxy" )}">How to Cite Galaxy</a></li>
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</ul>
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</div>
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</td>
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@@ -107,9 +107,9 @@
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<%
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menu_options = [
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['Email comments, bug reports, or suggestions', app.config.get( "bugs_email", "mailto:galaxy-bugs@bx.psu.edu" ) ],
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['Galaxy Wiki', app.config.get( "wiki_url", "http://bitbucket.org/galaxy/galaxy-central/wiki" ), "_blank" ],
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['Galaxy Wiki', app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ],
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['Video tutorials (screencasts)', app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ],
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['How to Cite Galaxy', app.config.get( "screencasts_url", "http://bitbucket.org/galaxy/galaxy-central/wiki/Citations" ), "_blank" ]
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['How to Cite Galaxy', app.config.get( "screencasts_url", "templates/webapps/galaxy/base_panels.mako" ), "_blank" ]
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]
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tab( "help", "Help", None, menu_options=menu_options)
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%>
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@@ -109,7 +109,7 @@ Organisms in **bold** are available at the UCSC Browser.
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**Note:** Having trouble locating your organism? Click here_ for a list of available species and their location.
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.. _here: http://bitbucket.org/galaxy/galaxy-central/wiki/Microbes
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.. _here: http://wiki.g2.bx.psu.edu/Main/Data%20Libraries/Microbes
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</help>
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</tool>
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@@ -34,7 +34,7 @@ This operation counts the total bases covered by a set of intervals. Bases that
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See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
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.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
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</help>
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@@ -67,7 +67,7 @@
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See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
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.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
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-----
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@@ -43,7 +43,7 @@ This operation complements the regions of a set of intervals. Regions are retur
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See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
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.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
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-----
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@@ -41,7 +41,7 @@
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See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
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.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
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-----
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@@ -44,7 +44,7 @@ Find the coverage of intervals in the first dataset on intervals in the second d
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See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
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.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
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-----
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@@ -117,7 +117,7 @@
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See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
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.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
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-----
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@@ -78,7 +78,7 @@
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See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
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.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
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-----
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@@ -44,7 +44,7 @@
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See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
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.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
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-----
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@@ -98,7 +98,7 @@
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See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
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.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
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.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
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-----
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@@ -75,7 +75,7 @@ Galaxy pipeline for mapping of Illumina data requires data to be in fastq format
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A good description of fastq datasets can be found `here`__, while a description of Galaxy's fastq "logic" can be found `here`__. Because ranges of quality values within different types of fastq datasets overlap it very difficult to detect them automatically. This tool supports conversion of two commonly found types (Solexa/Illumina 1.0 and Illumina 1.3+) into fastq Sanger.
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.. __: http://en.wikipedia.org/wiki/FASTQ_format
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.. __: http://bitbucket.org/galaxy/galaxy-central/wiki/NGS
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.. __: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
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.. class:: warningmark
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@@ -3,7 +3,7 @@
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# environment. To tune the application for a multi-user production
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# environment, see the documentation at:
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#
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# http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer
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# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server
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#
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# Throughout this sample configuration file, except where stated otherwise,
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@@ -129,7 +129,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
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# Directory where data used by tools is located, see the samples in that
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# directory and the wiki for help:
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# http://bitbucket.org/galaxy/galaxy-central/wiki/DataIntegration
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# http://galaxyproject.org/wiki/Admin/Data%20Integration
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#tool_data_path = tool-data
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# Directory where chrom len files are kept, currently mainly used by trackster
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@@ -208,13 +208,13 @@ nglims_config_file = tool-data/nglims.yaml
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#logo_url = /
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# The URL linked by the "Galaxy Wiki" link in the "Help" menu.
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#wiki_url = http://bitbucket.org/galaxy/galaxy-central/wiki
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#wiki_url = http://wiki.g2.bx.psu.edu/
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# The URL linked by the "Email comments..." link in the "Help" menu.
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#bugs_email = mailto:galaxy-bugs@bx.psu.edu
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# The URL linked by the "How to Cite..." link in the "Help" menu.
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#citation_url = http://bitbucket.org/galaxy/galaxy-central/wiki/Citations
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#citation_url = http://galaxyproject.org/wiki/Citing%20Galaxy
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# Serve static content, which must be enabled if you're not serving it via a
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# proxy server. These options should be self explanatory and so are not
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@@ -314,7 +314,7 @@ use_interactive = True
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# -- Data Libraries
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# These library upload options are described in much more detail in the wiki:
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# http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles
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# http://galaxyproject.org/wiki/Admin/Data%20Libraries/Uploading%20Library%20Files
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# Add an option to the library upload form which allows administrators to
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# upload a directory of files.
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@@ -372,7 +372,7 @@ use_interactive = True
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# User authentication can be delegated to an upstream proxy server (usually
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# Apache). The upstream proxy should set a REMOTE_USER header in the request.
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# Enabling remote user disables regular logins. For more information, see:
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# http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy
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# http://galaxyproject.org/wiki/Admin/Config/Apache%20Proxy
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#use_remote_user = False
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# If use_remote_user is enabled and your external authentication
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@@ -388,7 +388,7 @@ use_interactive = True
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# users (email addresses). These users will have access to the Admin section
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# of the server, and will have access to create users, groups, roles,
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# libraries, and more. For more information, see:
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# http://bitbucket.org/galaxy/galaxy-central/wiki/Admin/AdminInterface
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# http://wiki.g2.bx.psu.edu/Admin/Interface
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#admin_users = None
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# Force everyone to log in (disable anonymous access).
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@@ -454,7 +454,7 @@ use_interactive = True
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# If running multiple Galaxy processes, one can be designated as the job
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# runner. For more information, see:
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# http://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling
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# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling
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#enable_job_running = True
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# Should jobs be tracked through the database, rather than in memory.
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@@ -505,7 +505,7 @@ use_interactive = True
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# Clustering Galaxy is not a straightforward process and requires some
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# pre-configuration. See the the wiki before attempting to set any of these
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# options:
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# http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
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# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
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# Comma-separated list of job runners to start. local is always started. If
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# left commented, no jobs will be run on the cluster, even if a cluster URL is
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Reference in New Issue
Block a user