update Main mutable confs, installed bunch of samtools

galaxyproject · Dec 22, 2015 · a9ea64b · a9ea64b
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diff --git a/files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml b/files/galaxy/usegalaxy.org/var/integrated_tool_panel.xml
@@ -201,6 +201,12 @@
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/tophat_fusion_post/tophat_fusion_post/0.1" />
     </section>
     <section id="samtools" name="NGS: SAMtools" version="">
+        <tool id="toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.7.1" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.2" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.1" />
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1" />
         <tool id="toolshed.g2.bx.psu.edu/repos/gregory-minevich/bcftools_view/bcftools_view/0.0.1" />
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/samtools_reheader/samtools_reheader/2.0" />
@@ -233,6 +239,9 @@
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/1.1.3" />
     </section>
     <section id="ngs:_bam_tools" name="NGS: BamTools" version="">
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/0.0.2" />
+        <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/0.0.2" />
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.1" />
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/0.0.1" />
         <tool id="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/0.0.1" />

diff --git a/files/galaxy/usegalaxy.org/var/shed_tool_conf.xml b/files/galaxy/usegalaxy.org/var/shed_tool_conf.xml
@@ -4475,4 +4475,114 @@
     </tool>
 </section>
 
+<section id="samtools" name="NGS: SAMtools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/bfc4517aa037/samtools_mpileup/samtools_mpileup.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>samtools_mpileup</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>bfc4517aa037</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/2.1.1</id>
+        <version>2.1.1</version>
+    </tool>
+</section>
+
+<section id="samtools" name="NGS: SAMtools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/ef11139d4545/pileup_interval/pileup_interval.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.2">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>pileup_interval</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>ef11139d4545</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/pileup_interval/pileup_interval/1.0.2</id>
+        <version>1.0.2</version>
+    </tool>
+</section>
+
+<section id="ngs:_bam_tools" name="NGS: BamTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/4555f451dd79/bamtools_split/bamtools-split.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/0.0.2">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>bamtools_split</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>4555f451dd79</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/bamtools_split/bamSplit/0.0.2</id>
+        <version>0.0.2</version>
+    </tool>
+</section>
+
+<section id="ngs:_bam_tools" name="NGS: BamTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/2098a49ddf66/bamtools_filter/bamtools-filter.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/0.0.2">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>bamtools_filter</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>2098a49ddf66</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/0.0.2</id>
+        <version>0.0.2</version>
+    </tool>
+</section>
+
+<section id="ngs:_bam_tools" name="NGS: BamTools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/bamtools/ea3fc1adee75/bamtools/bamtools.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>bamtools</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>ea3fc1adee75</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/bamtools/bamtools/0.0.2</id>
+        <version>0.0.2</version>
+    </tool>
+</section>
+
+<section id="samtools" name="NGS: SAMtools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/8187a729d9f4/ngsutils_bam_filter/bam_filter.xml" guid="toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.7.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>ngsutils_bam_filter</repository_name>
+        <repository_owner>iuc</repository_owner>
+        <installed_changeset_revision>8187a729d9f4</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/iuc/ngsutils_bam_filter/ngsutils_bam_filter/0.5.7.1</id>
+        <version>0.5.7.1</version>
+    </tool>
+</section>
+
+<section id="samtools" name="NGS: SAMtools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/881e16ad05c6/sam_to_bam/sam_to_bam.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>sam_to_bam</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>881e16ad05c6</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/sam_to_bam/2.1</id>
+        <version>2.1</version>
+    </tool>
+</section>
+
+<section id="samtools" name="NGS: SAMtools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/bb40e4252392/samtools_rmdup/samtools_rmdup.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>samtools_rmdup</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>bb40e4252392</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/samtools_rmdup/samtools_rmdup/2.0</id>
+        <version>2.0</version>
+    </tool>
+</section>
+
+<section id="samtools" name="NGS: SAMtools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/1977f1637890/sam_merge/sam_merge.xml" guid="toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>sam_merge</repository_name>
+        <repository_owner>devteam</repository_owner>
+        <installed_changeset_revision>1977f1637890</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/devteam/sam_merge/sam_merge2/1.2.0</id>
+        <version>1.2.0</version>
+    </tool>
+</section>
+
+<section id="samtools" name="NGS: SAMtools" version="">
+  <tool file="toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/ac70bfaf1224/filter_on_md/MDtag_filter.xml" guid="toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2">
+      <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+        <repository_name>filter_on_md</repository_name>
+        <repository_owner>boris</repository_owner>
+        <installed_changeset_revision>ac70bfaf1224</installed_changeset_revision>
+        <id>toolshed.g2.bx.psu.edu/repos/boris/filter_on_md/MDtag_filter/1.0.2</id>
+        <version>1.0.2</version>
+    </tool>
+</section>
+
 </toolbox>
diff --git a/files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml b/files/galaxy/usegalaxy.org/var/shed_tool_data_table_conf.xml
@@ -380,4 +380,34 @@
             <installed_changeset_revision>6d4d39720545</installed_changeset_revision>
             </tool_shed_repository>
     </table>
+<table comment_char="#" name="fasta_indexes">
+        <columns>value, dbkey, name, path</columns>
+        <file path="/galaxy-repl/main/tool_data/toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/bfc4517aa037/fasta_indexes.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>samtools_mpileup</repository_name>
+            <repository_owner>devteam</repository_owner>
+            <installed_changeset_revision>bfc4517aa037</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="sam_fa_indexes">
+        <columns>line_type, value, path</columns>
+        <file path="/galaxy-repl/main/tool_data/toolshed.g2.bx.psu.edu/repos/devteam/bamtools/ea3fc1adee75/sam_fa_indices.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>bamtools</repository_name>
+            <repository_owner>devteam</repository_owner>
+            <installed_changeset_revision>ea3fc1adee75</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
+<table comment_char="#" name="fasta_indexes">
+        <columns>value, dbkey, name, path</columns>
+        <file path="/galaxy-repl/main/tool_data/toolshed.g2.bx.psu.edu/repos/devteam/sam_to_bam/881e16ad05c6/fasta_indexes.loc" />
+        <tool_shed_repository>
+            <tool_shed>toolshed.g2.bx.psu.edu</tool_shed>
+            <repository_name>sam_to_bam</repository_name>
+            <repository_owner>devteam</repository_owner>
+            <installed_changeset_revision>881e16ad05c6</installed_changeset_revision>
+            </tool_shed_repository>
+    </table>
 </tables>