Mutable configs on Test

galaxyproject · Apr 29, 2015 · 467a9cc · 467a9cc
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Showing 4 changed files with 60 additions and 31 deletions.
diff --git a/files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml b/files/galaxy/test.galaxyproject.org/var/integrated_tool_panel.xml
@@ -754,6 +754,7 @@
         <tool id="toolshed.g2.bx.psu.edu/repos/arkarachai-fungtammasan/microsatellite_ngs/heteroprob/2.0.0" />
     </section>
     <section id="metagenomics" name="Metagenomics" version="">
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/cd_hit_dup/cd_hit_dup/0.0.1" />
         <tool id="testtoolshed.g2.bx.psu.edu/repos/devteam/kraken_translate/kraken-translate/1.0.0" />
         <tool id="testtoolshed.g2.bx.psu.edu/repos/devteam/kraken/kraken/1.0.0" />
         <tool id="testtoolshed.g2.bx.psu.edu/repos/devteam/kraken_report/kraken-report/1.0.0" />

diff --git a/files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml b/files/galaxy/test.galaxyproject.org/var/shed_data_manager_conf.xml
@@ -28,6 +28,8 @@
 
 
 
+
+
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/data_manager/data_manager_gemini_download/0.0.1" id="data_manager_gemini_download" shed_conf_file="/srv/galaxy/test/var/shed_tool_conf.xml">
         <tool file="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/a580422f6f1d/data_manager_gemini_database_downloader/data_manager/data_manager_gemini_download.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/data_manager_gemini_download/0.10.0"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_gemini_database_downloader</repository_name><repository_owner>iuc</repository_owner><installed_changeset_revision>a580422f6f1d</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/iuc/data_manager_gemini_database_downloader/data_manager_gemini_download/0.10.0</id><version>0.10.0</version></tool><data_table name="gemini_databases">  <!-- Defines a Data Table to be modified. -->
             <output> <!-- Handle the output of the Data Manager Tool -->
@@ -53,6 +55,8 @@
 
 
 
+
+
 <data_manager guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/data_manager/sam_fasta_index_builder/0.0.1" id="sam_fasta_index_builder" shed_conf_file="/srv/galaxy/test/var/shed_tool_conf.xml" version="0.0.1">
         <tool file="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/cf875cbe2df4/data_manager_sam_fasta_index_builder/data_manager/data_manager_sam_fasta_index_builder.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/sam_fasta_index_builder/0.0.2"><tool_shed>toolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_sam_fasta_index_builder</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>cf875cbe2df4</installed_changeset_revision><id>toolshed.g2.bx.psu.edu/repos/devteam/data_manager_sam_fasta_index_builder/sam_fasta_index_builder/0.0.2</id><version>0.0.2</version></tool><data_table name="fasta_indexes">
             <output>
@@ -74,6 +78,8 @@
 
 
 
+
+
 <data_manager guid="testtoolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/data_manager/kraken_database_builder/1.0.0" id="kraken_database_builder" shed_conf_file="/srv/galaxy/test/var/shed_tool_conf.xml" version="1.0.0">
         <tool file="testtoolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/d5d803e654dd/data_manager_build_kraken_database/data_manager/kraken_database_builder.xml" guid="testtoolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/kraken_database_builder/1.0.0"><tool_shed>testtoolshed.g2.bx.psu.edu</tool_shed><repository_name>data_manager_build_kraken_database</repository_name><repository_owner>devteam</repository_owner><installed_changeset_revision>d5d803e654dd</installed_changeset_revision><id>testtoolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/kraken_database_builder/1.0.0</id><version>1.0.0</version></tool><data_table name="kraken_databases">
             <output>

diff --git a/files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml b/files/galaxy/test.galaxyproject.org/var/shed_tool_conf.xml
@@ -5729,36 +5729,48 @@
 
 <section id="structurefold" name="RNA Structure Prediction">
   <tool file="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/7bb98e9296e9/structurefold/Iterative_mapping/iterative_map.xml" guid="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/iterative_map_pipeline/1.0">
-    <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
-    <repository_name>structurefold</repository_name>
-    <repository_owner>tyty</repository_owner>
-    <installed_changeset_revision>7bb98e9296e9</installed_changeset_revision>
-    <id>toolshed.g2.bx.psu.edu/repos/tyty/structurefold/iterative_map_pipeline/1.0</id>
-    <version>1.0</version>
-  </tool>
-  <tool file="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/7bb98e9296e9/structurefold/get_reads/get_read.xml" guid="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/get_read_pipeline/1.0">
-    <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
-    <repository_name>structurefold</repository_name>
-    <repository_owner>tyty</repository_owner>
-    <installed_changeset_revision>7bb98e9296e9</installed_changeset_revision>
-    <id>toolshed.g2.bx.psu.edu/repos/tyty/structurefold/get_read_pipeline/1.0</id>
-    <version>1.0</version>
-  </tool>
-  <tool file="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/7bb98e9296e9/structurefold/reactivity_cal/reactivity_calculation.xml" guid="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/react_cal_pipeline/1.0">
-    <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
-    <repository_name>structurefold</repository_name>
-    <repository_owner>tyty</repository_owner>
-    <installed_changeset_revision>7bb98e9296e9</installed_changeset_revision>
-    <id>toolshed.g2.bx.psu.edu/repos/tyty/structurefold/react_cal_pipeline/1.0</id>
-    <version>1.0</version>
-  </tool>
-  <tool file="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/7bb98e9296e9/structurefold/predict/predict_RNAs.xml" guid="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/predict_pipeline/1.0">
-    <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
-    <repository_name>structurefold</repository_name>
-    <repository_owner>tyty</repository_owner>
-    <installed_changeset_revision>7bb98e9296e9</installed_changeset_revision>
-    <id>toolshed.g2.bx.psu.edu/repos/tyty/structurefold/predict_pipeline/1.0</id>
-    <version>1.0</version>
-  </tool>
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>structurefold</repository_name>
+        <repository_owner>tyty</repository_owner>
+        <installed_changeset_revision>7bb98e9296e9</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/tyty/structurefold/iterative_map_pipeline/1.0</id>
+        <version>1.0</version>
+    </tool>
+    <tool file="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/7bb98e9296e9/structurefold/get_reads/get_read.xml" guid="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/get_read_pipeline/1.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>structurefold</repository_name>
+        <repository_owner>tyty</repository_owner>
+        <installed_changeset_revision>7bb98e9296e9</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/tyty/structurefold/get_read_pipeline/1.0</id>
+        <version>1.0</version>
+    </tool>
+    <tool file="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/7bb98e9296e9/structurefold/reactivity_cal/reactivity_calculation.xml" guid="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/react_cal_pipeline/1.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>structurefold</repository_name>
+        <repository_owner>tyty</repository_owner>
+        <installed_changeset_revision>7bb98e9296e9</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/tyty/structurefold/react_cal_pipeline/1.0</id>
+        <version>1.0</version>
+    </tool>
+    <tool file="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/7bb98e9296e9/structurefold/predict/predict_RNAs.xml" guid="toolshed.g2.bx.psu.edu/repos/tyty/structurefold/predict_pipeline/1.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>structurefold</repository_name>
+        <repository_owner>tyty</repository_owner>
+        <installed_changeset_revision>7bb98e9296e9</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/tyty/structurefold/predict_pipeline/1.0</id>
+        <version>1.0</version>
+    </tool>
+</section>
+
+<section id="metagenomics" name="Metagenomics" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/cd_hit_dup/2e150ed1b76e/cd_hit_dup/cd_hit_dup.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/cd_hit_dup/cd_hit_dup/0.0.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>cd_hit_dup</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>2e150ed1b76e</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/cd_hit_dup/cd_hit_dup/0.0.1</id>
+        <version>0.0.1</version>
+    </tool>
 </section>
+
 </toolbox>
diff --git a/files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml b/files/galaxy/test.galaxyproject.org/var/shed_tool_data_table_conf.xml
@@ -760,4 +760,14 @@
             <installed_changeset_revision>0d71d9467847</installed_changeset_revision>
             </tool_shed_repository>
     </table>
+<table comment_char="#" name="kraken_databases">
+        <columns>value, name, path</columns>
+        <file path="/galaxy-repl/test/tool_data/testtoolshed.g2.bx.psu.edu/repos/devteam/data_manager_build_kraken_database/d5d803e654dd/kraken_databases.loc" />
+        <tool_shed_repository>
+            <tool_shed>testtoolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>data_manager_build_kraken_database</repository_name>
+            <repository_owner>devteam</repository_owner>
+            <installed_changeset_revision>d5d803e654dd</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
 </tables>