Install Bowtie2 2.3.4.2 and Diffbind 2.6.6.4 on Test and Main. Remove…

… Diffbind 2.6.6.3 from Main
galaxyproject · Jun 7, 2018 · 703b5c1 · 703b5c1
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Showing 6 changed files with 71 additions and 12 deletions.
diff --git a/env/main/files/galaxy/var/integrated_tool_panel.xml b/env/main/files/galaxy/var/integrated_tool_panel.xml
@@ -639,6 +639,8 @@
 
     <section id="ngs_mapping" name="NGS: Mapping" version="">
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_wrapper_2/1.3.2" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/lastz/lastz_d_wrapper/1.3.2" />
@@ -1229,7 +1231,7 @@
 
     <section id="peak_calling" name="NGS: Peak Calling" version="">
 
-        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.3" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.4" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.5.0" />
 

diff --git a/env/main/files/galaxy/var/shed_tool_conf.xml b/env/main/files/galaxy/var/shed_tool_conf.xml
@@ -15266,17 +15266,6 @@
     </tool>
 </section>
 
-<section id="peak_calling" name="NGS: Peak Calling" version="">
-  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/1de83981d43c/diffbind/diffbind.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.3">
-      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
-        <repository_name>diffbind</repository_name>
-        <repository_owner>bgruening</repository_owner>
-        <installed_changeset_revision>1de83981d43c</installed_changeset_revision>
-        <id>toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.3</id>
-        <version>2.6.6.3</version>
-    </tool>
-</section>
-
 <section id="samtools" name="NGS: SAMtools" version="">
   <tool file="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/b03984136ce4/bcftools_call/bcftools_call.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/bcftools_call/bcftools_call/1.4.0">
       <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
@@ -15299,4 +15288,26 @@
     </tool>
 </section>
 
+<section id="ngs_mapping" name="NGS: Mapping" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/17062a0decb7/bowtie2/bowtie2_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>bowtie2</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>17062a0decb7</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2</id>
+        <version>2.3.4.2</version>
+    </tool>
+</section>
+
+<section id="peak_calling" name="NGS: Peak Calling" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/c97a786e8fb5/diffbind/diffbind.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.4">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>diffbind</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>c97a786e8fb5</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.4</id>
+        <version>2.6.6.4</version>
+    </tool>
+</section>
+
 </toolbox>
diff --git a/env/main/files/galaxy/var/shed_tool_data_table_conf.xml b/env/main/files/galaxy/var/shed_tool_data_table_conf.xml
@@ -13010,4 +13010,14 @@
             <installed_changeset_revision>07e71cf6c8ef</installed_changeset_revision>
             </tool_shed_repository>
     </table>
+<table comment_char="#" name="bowtie2_indexes">
+        <columns>value, dbkey, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/17062a0decb7/bowtie2_indices.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>bowtie2</repository_name>
+            <repository_owner>devteam</repository_owner>
+            <installed_changeset_revision>17062a0decb7</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
 </tables>
diff --git a/env/test/files/galaxy/var/integrated_tool_panel.xml b/env/test/files/galaxy/var/integrated_tool_panel.xml
@@ -405,6 +405,8 @@
 
     <section id="solexa_tools" name="NGS: Mapping" version="">
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/megablast_xml_parser/megablast_xml_parser/1.0.0" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/megablast_wrapper/megablast_wrapper/1.2.0" />
@@ -1759,6 +1761,8 @@
 
     <section id="peak_calling" name="NGS: Peak Calling" version="">
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.4" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.5.0" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/repmatch_gff3/repmatch_gff3/1.0.0" />

diff --git a/env/test/files/galaxy/var/shed_tool_conf.xml b/env/test/files/galaxy/var/shed_tool_conf.xml
@@ -8426,4 +8426,26 @@
     </tool>
 </section>
 
+<section id="solexa_tools" name="NGS: Mapping" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/17062a0decb7/bowtie2/bowtie2_wrapper.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>bowtie2</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>17062a0decb7</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/bowtie2/2.3.4.2</id>
+        <version>2.3.4.2</version>
+    </tool>
+</section>
+
+<section id="peak_calling" name="NGS: Peak Calling" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/c97a786e8fb5/diffbind/diffbind.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.4">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>diffbind</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>c97a786e8fb5</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/diffbind/diffbind/2.6.6.4</id>
+        <version>2.6.6.4</version>
+    </tool>
+</section>
+
 </toolbox>
diff --git a/env/test/files/galaxy/var/shed_tool_data_table_conf.xml b/env/test/files/galaxy/var/shed_tool_data_table_conf.xml
@@ -2870,4 +2870,14 @@
             <installed_changeset_revision>6ab42baa56e9</installed_changeset_revision>
             </tool_shed_repository>
     </table>
+<table comment_char="#" name="bowtie2_indexes">
+        <columns>value, dbkey, name, path</columns>
+        <file path="/cvmfs/test.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/devteam/bowtie2/17062a0decb7/bowtie2_indices.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>bowtie2</repository_name>
+            <repository_owner>devteam</repository_owner>
+            <installed_changeset_revision>17062a0decb7</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
 </tables>