diff --git a/README.txt b/README.txt
index 9496410db7b..fd2f7f88bb9 100644
--- a/README.txt
+++ b/README.txt
@@ -28,4 +28,4 @@ on adding tools can be found on the Galaxy website (linked above).
Not all dependencies are included for the tools provided in the sample
tool_conf.xml. A full list of external dependencies is available at:
-http://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies
+http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
diff --git a/dist-eggs.ini b/dist-eggs.ini
index d8bea3e3baf..61d370d5b7e 100644
--- a/dist-eggs.ini
+++ b/dist-eggs.ini
@@ -3,7 +3,7 @@
; eggs.g2.bx.psu.edu). Probably only useful to Galaxy developers at
; Penn State. This file is used by scripts/dist-scramble.py
;
-; More information: http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Eggs
+; More information: http://wiki.g2.bx.psu.edu/Admin/Config/Eggs
;
[hosts]
diff --git a/eggs.ini b/eggs.ini
index 0b9c5893c63..7bec53d8b6f 100644
--- a/eggs.ini
+++ b/eggs.ini
@@ -3,7 +3,7 @@
;
; This file is version controlled and should not be edited by hand!
; For more information, see:
-; http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Eggs
+; http://wiki.g2.bx.psu.edu/Admin/Config/Eggs
;
[general]
diff --git a/lib/galaxy/jobs/runners/pbs.py b/lib/galaxy/jobs/runners/pbs.py
index fee798ed069..11c4925a2c5 100644
--- a/lib/galaxy/jobs/runners/pbs.py
+++ b/lib/galaxy/jobs/runners/pbs.py
@@ -17,7 +17,7 @@ The 'pbs' runner depends on 'pbs_python' which is not installed or not
configured properly. Galaxy's "scramble" system should make this installation
simple, please follow the instructions found at:
- http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
+ http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
Additional errors may follow:
%s
diff --git a/lib/galaxy/jobs/runners/sge.py b/lib/galaxy/jobs/runners/sge.py
index 18b36fc8a41..c7b9f3f60ae 100644
--- a/lib/galaxy/jobs/runners/sge.py
+++ b/lib/galaxy/jobs/runners/sge.py
@@ -14,7 +14,7 @@ The 'sge' runner depends on 'DRMAA_python' which is not installed. Galaxy's
"scramble" system should make this installation simple, please follow the
instructions found at:
- http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
+ http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
Additional errors may follow:
%s
diff --git a/lib/galaxy/webapps/community/config.py b/lib/galaxy/webapps/community/config.py
index 7d290f2705d..fac2bacead5 100644
--- a/lib/galaxy/webapps/community/config.py
+++ b/lib/galaxy/webapps/community/config.py
@@ -64,7 +64,7 @@ class Configuration( object ):
self.nginx_upload_path = kwargs.get( 'nginx_upload_path', False )
self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) )
self.brand = kwargs.get( 'brand', None )
- self.wiki_url = kwargs.get( 'wiki_url', 'http://bitbucket.org/galaxy/galaxy-central/wiki/Home' )
+ self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' )
self.bugs_email = kwargs.get( 'bugs_email', None )
self.blog_url = kwargs.get( 'blog_url', None )
self.screencasts_url = kwargs.get( 'screencasts_url', None )
diff --git a/lib/galaxy/webapps/demo_sequencer/config.py b/lib/galaxy/webapps/demo_sequencer/config.py
index 518e44ebcf4..2111b6e76be 100644
--- a/lib/galaxy/webapps/demo_sequencer/config.py
+++ b/lib/galaxy/webapps/demo_sequencer/config.py
@@ -49,7 +49,7 @@ class Configuration( object ):
self.smtp_server = kwargs.get( 'smtp_server', None )
self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) )
self.brand = kwargs.get( 'brand', None )
- self.wiki_url = kwargs.get( 'wiki_url', 'http://bitbucket.org/galaxy/galaxy-central/wiki/Home' )
+ self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' )
self.bugs_email = kwargs.get( 'bugs_email', None )
self.blog_url = kwargs.get( 'blog_url', None )
self.screencasts_url = kwargs.get( 'screencasts_url', None )
diff --git a/lib/galaxy/webapps/reports/config.py b/lib/galaxy/webapps/reports/config.py
index a2f81f74243..4a69a4df78e 100644
--- a/lib/galaxy/webapps/reports/config.py
+++ b/lib/galaxy/webapps/reports/config.py
@@ -33,7 +33,7 @@ class Configuration( object ):
self.sendmail_path = kwargs.get('sendmail_path',"/usr/sbin/sendmail")
self.log_actions = string_as_bool( kwargs.get( 'log_actions', 'False' ) )
self.brand = kwargs.get( 'brand', None )
- self.wiki_url = kwargs.get( 'wiki_url', 'http://bitbucket.org/galaxy/galaxy-central/wiki/Home' )
+ self.wiki_url = kwargs.get( 'wiki_url', 'http://wiki.g2.bx.psu.edu/FrontPage' )
self.bugs_email = kwargs.get( 'bugs_email', None )
self.blog_url = kwargs.get( 'blog_url', None )
self.screencasts_url = kwargs.get( 'screencasts_url', None )
diff --git a/static/welcome.rst b/static/welcome.rst
index cd4df579915..685ea283ae1 100644
--- a/static/welcome.rst
+++ b/static/welcome.rst
@@ -30,7 +30,7 @@ Need Help?
.. __: /static/help.html
.. __: http://www.bx.psu.edu/cgi-bin/trac.cgi
-.. __: http://bitbucket.org/galaxy/galaxy-central/wiki/GalaxyTeam
+.. __: http://wiki.g2.bx.psu.edu/Galaxy%20Team
.. __: mailto:galaxy@bx.psu.edu
Version: 2.1 Revision: $Rev$
diff --git a/templates/webapps/community/base_panels.mako b/templates/webapps/community/base_panels.mako
index 8c5e3988942..ed1fd0a1e3f 100644
--- a/templates/webapps/community/base_panels.mako
+++ b/templates/webapps/community/base_panels.mako
@@ -34,9 +34,9 @@
diff --git a/templates/webapps/galaxy/base_panels.mako b/templates/webapps/galaxy/base_panels.mako
index f4a6334d65b..b8f04a23116 100644
--- a/templates/webapps/galaxy/base_panels.mako
+++ b/templates/webapps/galaxy/base_panels.mako
@@ -107,9 +107,9 @@
<%
menu_options = [
['Email comments, bug reports, or suggestions', app.config.get( "bugs_email", "mailto:galaxy-bugs@bx.psu.edu" ) ],
- ['Galaxy Wiki', app.config.get( "wiki_url", "http://bitbucket.org/galaxy/galaxy-central/wiki" ), "_blank" ],
+ ['Galaxy Wiki', app.config.get( "wiki_url", "http://wiki.g2.bx.psu.edu/" ), "_blank" ],
['Video tutorials (screencasts)', app.config.get( "screencasts_url", "http://galaxycast.org" ), "_blank" ],
- ['How to Cite Galaxy', app.config.get( "screencasts_url", "http://bitbucket.org/galaxy/galaxy-central/wiki/Citations" ), "_blank" ]
+ ['How to Cite Galaxy', app.config.get( "screencasts_url", "templates/webapps/galaxy/base_panels.mako" ), "_blank" ]
]
tab( "help", "Help", None, menu_options=menu_options)
%>
diff --git a/tools/data_source/microbial_import.xml b/tools/data_source/microbial_import.xml
index cbc112db33b..e6fd8be575f 100644
--- a/tools/data_source/microbial_import.xml
+++ b/tools/data_source/microbial_import.xml
@@ -109,7 +109,7 @@ Organisms in **bold** are available at the UCSC Browser.
**Note:** Having trouble locating your organism? Click here_ for a list of available species and their location.
-.. _here: http://bitbucket.org/galaxy/galaxy-central/wiki/Microbes
+.. _here: http://wiki.g2.bx.psu.edu/Main/Data%20Libraries/Microbes
diff --git a/tools/new_operations/basecoverage.xml b/tools/new_operations/basecoverage.xml
index e07ea37d029..5daf4aff402 100644
--- a/tools/new_operations/basecoverage.xml
+++ b/tools/new_operations/basecoverage.xml
@@ -34,7 +34,7 @@ This operation counts the total bases covered by a set of intervals. Bases that
See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
-.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
+.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
diff --git a/tools/new_operations/cluster.xml b/tools/new_operations/cluster.xml
index 829fd318397..9aa4c8a0172 100644
--- a/tools/new_operations/cluster.xml
+++ b/tools/new_operations/cluster.xml
@@ -67,7 +67,7 @@
See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
-.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
+.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
-----
diff --git a/tools/new_operations/complement.xml b/tools/new_operations/complement.xml
index c95a4fc247c..b7f6492775d 100644
--- a/tools/new_operations/complement.xml
+++ b/tools/new_operations/complement.xml
@@ -43,7 +43,7 @@ This operation complements the regions of a set of intervals. Regions are retur
See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
-.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
+.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
-----
diff --git a/tools/new_operations/concat.xml b/tools/new_operations/concat.xml
index bc19d577545..3bf51e118f9 100644
--- a/tools/new_operations/concat.xml
+++ b/tools/new_operations/concat.xml
@@ -41,7 +41,7 @@
See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
-.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
+.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
-----
diff --git a/tools/new_operations/coverage.xml b/tools/new_operations/coverage.xml
index 8915a71a8be..8dea61b3f49 100644
--- a/tools/new_operations/coverage.xml
+++ b/tools/new_operations/coverage.xml
@@ -44,7 +44,7 @@ Find the coverage of intervals in the first dataset on intervals in the second d
See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
-.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
+.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
-----
diff --git a/tools/new_operations/intersect.xml b/tools/new_operations/intersect.xml
index 8fa9e37397f..c5ed66d00ad 100644
--- a/tools/new_operations/intersect.xml
+++ b/tools/new_operations/intersect.xml
@@ -117,7 +117,7 @@
See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
-.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
+.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
-----
diff --git a/tools/new_operations/join.xml b/tools/new_operations/join.xml
index 1625447c458..c329378f613 100644
--- a/tools/new_operations/join.xml
+++ b/tools/new_operations/join.xml
@@ -78,7 +78,7 @@
See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
-.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
+.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
-----
diff --git a/tools/new_operations/merge.xml b/tools/new_operations/merge.xml
index 5cfd8d1ae62..e5a79196c2c 100644
--- a/tools/new_operations/merge.xml
+++ b/tools/new_operations/merge.xml
@@ -44,7 +44,7 @@
See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
-.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
+.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
-----
diff --git a/tools/new_operations/subtract.xml b/tools/new_operations/subtract.xml
index f036873a508..709eb91737b 100644
--- a/tools/new_operations/subtract.xml
+++ b/tools/new_operations/subtract.xml
@@ -98,7 +98,7 @@
See Galaxy Interval Operation Screencasts_ (right click to open this link in another window).
-.. _Screencasts: http://bitbucket.org/galaxy/galaxy-central/wiki/GopsDesc
+.. _Screencasts: http://wiki.g2.bx.psu.edu/Learn/Interval%20Operations
-----
diff --git a/tools/next_gen_conversion/fastq_gen_conv.xml b/tools/next_gen_conversion/fastq_gen_conv.xml
index 64c2be7a6fc..6eee981a591 100644
--- a/tools/next_gen_conversion/fastq_gen_conv.xml
+++ b/tools/next_gen_conversion/fastq_gen_conv.xml
@@ -75,7 +75,7 @@ Galaxy pipeline for mapping of Illumina data requires data to be in fastq format
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.
.. __: http://en.wikipedia.org/wiki/FASTQ_format
- .. __: http://bitbucket.org/galaxy/galaxy-central/wiki/NGS
+ .. __: http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
.. class:: warningmark
diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample
index c136c0879e1..b202a408842 100644
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -3,7 +3,7 @@
# environment. To tune the application for a multi-user production
# environment, see the documentation at:
#
-# http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer
+# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server
#
# Throughout this sample configuration file, except where stated otherwise,
@@ -129,7 +129,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
# Directory where data used by tools is located, see the samples in that
# directory and the wiki for help:
-# http://bitbucket.org/galaxy/galaxy-central/wiki/DataIntegration
+# http://galaxyproject.org/wiki/Admin/Data%20Integration
#tool_data_path = tool-data
# Directory where chrom len files are kept, currently mainly used by trackster
@@ -208,13 +208,13 @@ nglims_config_file = tool-data/nglims.yaml
#logo_url = /
# The URL linked by the "Galaxy Wiki" link in the "Help" menu.
-#wiki_url = http://bitbucket.org/galaxy/galaxy-central/wiki
+#wiki_url = http://wiki.g2.bx.psu.edu/
# The URL linked by the "Email comments..." link in the "Help" menu.
#bugs_email = mailto:galaxy-bugs@bx.psu.edu
# The URL linked by the "How to Cite..." link in the "Help" menu.
-#citation_url = http://bitbucket.org/galaxy/galaxy-central/wiki/Citations
+#citation_url = http://galaxyproject.org/wiki/Citing%20Galaxy
# Serve static content, which must be enabled if you're not serving it via a
# proxy server. These options should be self explanatory and so are not
@@ -314,7 +314,7 @@ use_interactive = True
# -- Data Libraries
# These library upload options are described in much more detail in the wiki:
-# http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles
+# http://galaxyproject.org/wiki/Admin/Data%20Libraries/Uploading%20Library%20Files
# Add an option to the library upload form which allows administrators to
# upload a directory of files.
@@ -372,7 +372,7 @@ use_interactive = True
# User authentication can be delegated to an upstream proxy server (usually
# Apache). The upstream proxy should set a REMOTE_USER header in the request.
# Enabling remote user disables regular logins. For more information, see:
-# http://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy
+# http://galaxyproject.org/wiki/Admin/Config/Apache%20Proxy
#use_remote_user = False
# If use_remote_user is enabled and your external authentication
@@ -388,7 +388,7 @@ use_interactive = True
# users (email addresses). These users will have access to the Admin section
# of the server, and will have access to create users, groups, roles,
# libraries, and more. For more information, see:
-# http://bitbucket.org/galaxy/galaxy-central/wiki/Admin/AdminInterface
+# http://wiki.g2.bx.psu.edu/Admin/Interface
#admin_users = None
# Force everyone to log in (disable anonymous access).
@@ -454,7 +454,7 @@ use_interactive = True
# If running multiple Galaxy processes, one can be designated as the job
# runner. For more information, see:
-# http://bitbucket.org/galaxy/galaxy-central/wiki/Config/WebApplicationScaling
+# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling
#enable_job_running = True
# Should jobs be tracked through the database, rather than in memory.
@@ -505,7 +505,7 @@ use_interactive = True
# Clustering Galaxy is not a straightforward process and requires some
# pre-configuration. See the the wiki before attempting to set any of these
# options:
-# http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster
+# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
# Comma-separated list of job runners to start. local is always started. If
# left commented, no jobs will be run on the cluster, even if a cluster URL is