Switch svn -> github

Author: bbimber

SequenceAnalysis/resources/views/siteAdmin.html

@@ -21,7 +21,7 @@
                     html: '<h3>Installation of Sequence Tools</h3>'
                 },{
                     html: 'DISCVR-Seq performs multiple functions, including management of data and analysis pipelines.  The latter requires many external tools, such as sequence aligners.<br><br>' +
-                        'Tools can be installed manually; however, we have created a bash script to facilitate installation of the core tools.  You can <b><a target="_blank" href="https://cpas:cpas@svn.mgt.labkey.host/stedi/trunk/externalModules/labModules/SequenceAnalysis/pipeline_code/sequence_tools_install.sh">download this script from subversion here</a></b>, using the username/password: cpas/cpas.  It can be executed using a command like:<br><br>' +
+                        'Tools can be installed manually; however, we have created a bash script to facilitate installation of the core tools.  You can <b><a target="_blank" href="https://raw.githubusercontent.com/BimberLab/DiscvrLabKeyModules/discvr-20.3/SequenceAnalysis/pipeline_code/sequence_tools_install.sh">download this script from github here</a></b>.  It can be executed using a command like:<br><br>' +
                         'bash sequence_tools_install.sh -d /usr/local/labkey/ -u labkey | tee sequence_tools_install.log<br><br>' +
                         'The command above will install the various tools into /usr/local/labkey/bin, using the user \'labkey\'.<br><br>'
                 },{
@@ -32,8 +32,8 @@
                             '<ul><li><a href="https://www.labkey.org/Documentation/wiki-page.view?name=installConfigureEnterprisePipeline">Install/Configure Enterprise Pipeline</a></li>' +
                             '<li><a href="https://www.labkey.org/Documentation/wiki-page.view?name=configureRemoteServer">Configure Remote Server</a></li></ul>' +
                             'Beyond the core configuration, you will need to perform several steps for DISCVR-Seq:' +
-                            '<ul><li>By default, all of the DISCVR-Seq\'s tasks will run locally (on the location \'webserver\'). This is so the module works out of the box on a given server. Changing this is done using a file comparable to the ms2Config.xml described in the \'Configure Remote Server\' link above. You will need to create the file \'sequenceanalysisConfig.xml\' in the /configs folder where your LK server is installed (i.e. /usr/local/labkey/configs/). <b><a href="https://cpas:cpas@svn.mgt.labkey.host/stedi/trunk/externalModules/labModules/SequenceAnalysis/tools/pipeline_config/sequenceanalysisConfig.xml">Click here to view an example config file with comments</a></b>. (use the username/password: cpas/cpas).  You will need to do this on both the webserver and remote server.</li>' +
-                            '<li>You will also need to configure the pipelineConfig.xml file on the remote server.  <b><a href="https://cpas:cpas@svn.mgt.labkey.host/stedi/trunk/externalModules/labModules/SequenceAnalysis/tools/pipeline_config/pipelineConfig_remote.xml">Click here to view an example with comments.</a></b>  Please note that you will need to configure the host name of the remote server to match the name you use in sequenceanalysisConfig.xml</li></ul>'
+                            '<ul><li>By default, all of the DISCVR-Seq\'s tasks will run locally (on the location \'webserver\'). This is so the module works out of the box on a given server. Changing this is done using a file comparable to the ms2Config.xml described in the \'Configure Remote Server\' link above. You will need to create the file \'sequenceanalysisConfig.xml\' in the /configs folder where your LK server is installed (i.e. /usr/local/labkey/configs/). <b><a href="https://raw.githubusercontent.com/BimberLab/DiscvrLabKeyModules/discvr-20.3/SequenceAnalysis/tools/pipeline_config/sequenceanalysisConfig.xml">Click here to view an example config file with comments</a></b>.  You will need to do this on both the webserver and remote server.</li>' +
+                            '<li>You will also need to configure the pipelineConfig.xml file on the remote server.  <b><a href="https://raw.githubusercontent.com/BimberLab/DiscvrLabKeyModules/discvr-20.3/SequenceAnalysis/tools/pipeline_config/pipelineConfig_remote.xml">Click here to view an example with comments.</a></b>  Please note that you will need to configure the host name of the remote server to match the name you use in sequenceanalysisConfig.xml</li></ul>'
                 },{
                     html: '<h3>Sequence Pipeline Validation</h3>'
                 },{