CLIMB customisation

m-bull · Apr 5, 2019 · c7c4e58 · c7c4e58
1 parent 4719f47
commit c7c4e58
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Showing 4 changed files with 78 additions and 5 deletions.
diff --git a/gvldash/static/images/climb-logo.png b/gvldash/static/images/climb-logo.png
diff --git a/gvldash/templates/pages/home.html b/gvldash/templates/pages/home.html
@@ -148,17 +148,60 @@ <h1>Public Services</h1>
                         <a target="_blank" href="https://usegalaxy.org.au">https://usegalaxy.org.au</a>
                     </td>
                 </tr>
+            </tbody>
+        </table>
+    </div>
+    <h1>CLIMB Services</h1>
+
+    <hr />
+    <div class="table-responsive">
+        <table class="table table-striped">
+            <thead>
+                <tr>
+                    <th></th>
+                    <th>Service Name</th>
+                    <th>Description</th>
+                    <th class="text-center">Status</th>
+                    <th>Access Link</th>
+                </tr>
+            </thead>
+            <tbody>
                 <tr>
-                    <td class="text-center"><a href="https://genomespace.gvl.org.au/jsui/" class="application-enabled"><img src="{% static 'images/logo_genomespace.png' %}"></a></td>
-                    <td>GVL GenomeSpace</td>
-                    <td>GenomeSpace is like dropbox, for genome data. Use GenomeSpace to store all your genomics
-                        data securely and redundantly.</td>
+                    <td class="text-center"><a href="https://climb.ac.uk" class="application-enabled"><img src="{% static 'images/climb-logo.png' %}"></a></td>
+                    <td>CLIMB Homepage</td>
+                    <td>Latest news and account requests</td>
                     <td>
                         <p class="text-success text-center">
                             <i class="fa fa-check-circle" title="Available"></i>
                         </p>
                     </td>
-                    <td><a target="_blank" href="https://genomespace.gvl.org.au/jsui/">https://genomespace.gvl.org.au</td>
+                    <td><a target="_blank" href="https:/climb.ac.uk">https://climb.ac.uk</a></td>
+                </tr>
+                <tr>
+                    <td class="text-center"><a href="https://bryn.climb.ac.uk" class="application-enabled"><img src="{% static 'images/climb-logo.png' %}"></a></td>
+                    <td>CLIMB Bryn</td>
+                    <td>Launch new GVL instances</td>
+                    <td>
+                        <p class="text-success text-center">
+                            <i class="fa fa-check-circle" title="Available"></i>
+                        </p>
+                    </td>
+                    <td>
+                        <a target="_blank" href="https://bryn.climb.ac.uk/">https://bryn.climb.ac.uk</a>
+                    </td>
+                </tr>
+                 <tr>
+                    <td class="text-center"><a href="https://discourse.climb.ac.uk" class="application-enabled"><img src="{% static 'images/climb-logo.png' %}"></a></td>
+                    <td>CLIMB Discourse</td>
+                    <td>Ask questions and report problems with the service</td>
+                    <td>
+                        <p class="text-success text-center">
+                            <i class="fa fa-check-circle" title="Available"></i>
+                        </p>
+                    </td>
+                    <td>
+                        <a target="_blank" href="https://discourse.climb.ac.uk/">https://discourse.climb.ac.uk</a>
+                    </td>
                 </tr>
             </tbody>
         </table>

diff --git a/tool_installation_scripts/install_cmdlineutils_package.sh b/tool_installation_scripts/install_cmdlineutils_package.sh
@@ -0,0 +1,15 @@
+#!/usr/bin/env bash
+################################################################################
+# script run on target machine to install the gal command line utilities package
+################################################################################
+
+[ -d "/mnt/gvl/apps" ] || mkdir -p /mnt/gvl/apps # ensure /mnt/galaxy/apps exists
+cd /opt/gvl
+if [ -d "/opt/gvl/gvl_commandline_utilities" ]; then 
+  cd /opt/gvl/gvl_commandline_utilities
+  git pull https://github.com/MRC-CLIMB/gvl_commandline_utilities
+else
+  git clone https://github.com/MRC-CLIMB/gvl_commandline_utilities
+fi
+chown -R ubuntu:ubuntu /opt/gvl/gvl_commandline_utilities
+sudo su - ubuntu -c "cd /opt/gvl/gvl_commandline_utilities; source run_all.sh -s"
diff --git a/tool_installation_scripts/install_smrt_analysis_package.sh b/tool_installation_scripts/install_smrt_analysis_package.sh
@@ -0,0 +1,15 @@
+#!/bin/bash
+###############################################################
+# script run on target machine to install smrt_analysis package
+###############################################################
+
+[ -d "/mnt/gvl/apps" ] || mkdir -p /mnt/gvl/apps # ensure /mnt/galaxy/apps exists
+cd /opt/gvl
+if [ -d "/opt/gvl/gvl.ansible.smrt_analysis" ]; then
+  cd /opt/gvl/gvl.ansible.smrt_analysis 
+  git pull https://github.com/MRC-CLIMB/gvl.ansible.smrt_analysis
+else
+  git clone https://github.com/MRC-CLIMB/gvl.ansible.smrt_analysis
+fi
+cd /opt/gvl/gvl.ansible.smrt_analysis
+ansible-playbook -i inventory/builders playbook.yml