Unicycler fixes for Main

galaxyproject · Oct 4, 2017 · 72a1d02 · 72a1d02
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commit 72a1d02
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,10 @@
 This is a log of any changes that were made manually that could not easily be codified in to Ansible. Changes made
 prior to the first entry have not been logged.
 
+### Wed Oct  4 12:59:53 EDT 2017
+
+Unicycler 0.4.1 has been installed on Bridges for Main using the process below (OpenJDK is shared between Test and Main).
+
 ### Tue Oct  3 14:20:57 EDT 2017
 
 Unicycler on Test was upgraded to 0.4.1 requiring roughly the same process as before, but the new version also checks

diff --git a/env/main/files/galaxy/var/integrated_tool_panel.xml b/env/main/files/galaxy/var/integrated_tool_panel.xml
@@ -711,6 +711,7 @@
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/gemini_de_novo/gemini_de_novo/0.18.1.0" />
     </section>
     <section id="ngs:_assembly" name="NGS: Assembly" version="">
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.1" />
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/quast/quast/4.1.1" />
         <tool id="toolshed.g2.bx.psu.edu/repos/crs4/prokka/prokka/1.12.0" />
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.2.0" />

diff --git a/env/main/files/galaxy/var/shed_tool_conf.xml b/env/main/files/galaxy/var/shed_tool_conf.xml
@@ -12130,4 +12130,15 @@
     </tool>
 </section>
 
+<section id="ngs:_assembly" name="NGS: Assembly" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/iuc/unicycler/f13d0498a199/unicycler/unicycler.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>unicycler</repository_name>
+        <repository_owner>iuc</repository_owner>
+        <installed_changeset_revision>f13d0498a199</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/iuc/unicycler/unicycler/0.4.1</id>
+        <version>0.4.1</version>
+    </tool>
+</section>
+
 </toolbox>
diff --git a/env/main/templates/galaxy/config/job_conf.xml.j2 b/env/main/templates/galaxy/config/job_conf.xml.j2
@@ -360,6 +360,7 @@
             <param id="file_action_config">{{ galaxy_config_dir }}/pulsar_bridges_actions.yml</param>
             <env exec="eval `modulecmd sh purge`" />
             <!-- https://bugs.openjdk.java.net/browse/JDK-7085890 -->
+            <env id="PATH">/pylon5/mc48nsp/xcgalaxy/openjdk8/bin:$PATH</env>
             <env id="_JAVA_OPTIONS">-Dsun.zip.disableMemoryMapping=true</env>
         </xml>
         <xml name="multi_tool" tokens="id">