diff --git a/env/main/files/galaxy/var/integrated_tool_panel.xml b/env/main/files/galaxy/var/integrated_tool_panel.xml
index 1ec5c30f6..3ca86b985 100644
--- a/env/main/files/galaxy/var/integrated_tool_panel.xml
+++ b/env/main/files/galaxy/var/integrated_tool_panel.xml
@@ -321,6 +321,8 @@
 
     <section id="cshl_library_information" name="NGS: QC and manipulation" version="">
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.1" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/flash/flash/1.2.11.3" />
@@ -767,6 +769,12 @@
 
     <section id="ngs-rna-tools" name="NGS: RNA Analysis" version="">
 
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.11.2" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/0.8.24" />
+
+        <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/0.8.24.1" />
+
         <tool id="toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.9.1" />
 
         <tool id="toolshed.g2.bx.psu.edu/repos/iuc/kallisto_quant/kallisto_quant/0.43.1.3" />
diff --git a/env/main/files/galaxy/var/shed_tool_conf.xml b/env/main/files/galaxy/var/shed_tool_conf.xml
index 3099905b3..b334c3e76 100644
--- a/env/main/files/galaxy/var/shed_tool_conf.xml
+++ b/env/main/files/galaxy/var/shed_tool_conf.xml
@@ -17293,4 +17293,45 @@
     </tool>
 </section>
 
+<section id="cshl_library_information" name="NGS: QC and manipulation" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/iuc/pear/2f804526f5fd/pear/pear.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>pear</repository_name>
+        <repository_owner>iuc</repository_owner>
+        <installed_changeset_revision>2f804526f5fd</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/iuc/pear/iuc_pear/0.9.6.1</id>
+        <version>0.9.6.1</version>
+    </tool>
+</section>
+
+<section id="ngs-rna-tools" name="NGS: RNA Analysis" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/diamond/3c6b132b154a/diamond/diamond_makedb.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/0.8.24">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>diamond</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>3c6b132b154a</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond_makedb/0.8.24</id>
+        <version>0.8.24</version>
+    </tool>
+    <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/diamond/3c6b132b154a/diamond/diamond.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/0.8.24.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>diamond</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>3c6b132b154a</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/diamond/bg_diamond/0.8.24.1</id>
+        <version>0.8.24.1</version>
+    </tool>
+</section>
+
+<section id="ngs-rna-tools" name="NGS: RNA Analysis" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/bgruening/salmon/6b0ba6de1424/salmon/salmon.xml" guid="toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.11.2">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>salmon</repository_name>
+        <repository_owner>bgruening</repository_owner>
+        <installed_changeset_revision>6b0ba6de1424</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.11.2</id>
+        <version>0.11.2</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
index 937cff6fa..ce369df86 100644
--- a/env/main/files/galaxy/var/shed_tool_data_table_conf.xml
+++ b/env/main/files/galaxy/var/shed_tool_data_table_conf.xml
@@ -13570,4 +13570,24 @@
             <installed_changeset_revision>57e5d9382f36</installed_changeset_revision>
             </tool_shed_repository>
     </table>
+<table comment_char="#" name="diamond_database">
+        <columns>value, name, db_path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/diamond/3c6b132b154a/diamond_database.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>diamond</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>3c6b132b154a</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="salmon_indexes">
+        <columns>value, name, path</columns>
+        <file path="/cvmfs/main.galaxyproject.org/tool_data/toolshed.g2.bx.psu.edu/repos/bgruening/salmon/6b0ba6de1424/salmon_indexes.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>salmon</repository_name>
+            <repository_owner>bgruening</repository_owner>
+            <installed_changeset_revision>6b0ba6de1424</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
 </tables>