Mercurial > repos > rnateam > blockclust

changeset 6:b77328c96ac9 draft

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Uploaded
author rnateam
date Tue, 22 Oct 2013 11:27:29 -0400
parents 49b72f1013b3
children a2aed24f5846
files blockclust.xml tool_dependencies.xml
diffstat 2 files changed, 12 insertions(+), 7 deletions(-) [+]
line wrap: on
line diff
--- a/blockclust.xml	Tue Oct 22 10:15:09 2013 -0400
+++ b/blockclust.xml	Tue Oct 22 11:27:29 2013 -0400
@@ -10,6 +10,7 @@
     <!--<version_command> -version</version_command>-->
     <command>
         #set $blockclust_data_path = \$BLOCKCLUST_DATA_PATH
+
         #if str($mode.operation) == "pre":
             #set $outputdir = $tags_bed.extra_files_path
             BlockClustPipeLine.pl -m PRE -bam $mode.reads_bam -tbed $tags_bed;
@@ -42,7 +43,7 @@
     
         #if str($mode.operation) == "post":
             #set $outputdir = $clusters_bed.extra_files_path
-            BlockClustPipeLine.pl -m POST -cbed $mode.clusters_bed -cm $mode.cmsearch_out -tab $mode.sim_tab_in -o $outputdir;
+            BlockClustPipeLine.pl -m POST -cbed $mode.clusters_bed -cm $mode.cmsearch_out -tab $mode.sim_tab_in -o $outputdir -rfam $blockclust_data_path/rfam_map.txt;
             cp #echo os.path.join($outputdir, 'cluster_distribution.pdf')# $cluster_dist;
         #end if
     </command>
--- a/tool_dependencies.xml	Tue Oct 22 10:15:09 2013 -0400
+++ b/tool_dependencies.xml	Tue Oct 22 11:27:29 2013 -0400
@@ -1,6 +1,9 @@
 <?xml version="1.0"?>
 <tool_dependency>
-   <package name="blockclust" version="1.0">
+    <package name="samtools" version="0.1.19">
+        <repository changeset_revision="54195f1d4b0f" name="package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="blockclust" version="1.0">
         <install version="1.0">
             <actions>
                 <action type="download_by_url">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-1.0.tar.gz</action>
@@ -21,6 +24,10 @@
                     <source>blockclust.config</source>
                     <destination>$INSTALL_DIR/data/</destination>
                 </action>
+                <action type="move_file">
+                    <source>rfam_map.txt</source>
+                    <destination>$INSTALL_DIR/data/</destination>
+                </action>
                 <action type="make_directory">$INSTALL_DIR/data/annotations</action>
                 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/dm3.tar.gz</action>
                 <action type="shell_command">tar xfvz dm3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
@@ -33,16 +40,13 @@
                 <action type="download_file">https://github.com/bgruening/download_store/raw/master/blockclust/blockclust-data-1.0/annotations/rheMac3.tar.gz</action>
                 <action type="shell_command">tar xfvz rheMac3.tar.gz -C $INSTALL_DIR/data/annotations/</action>
                 <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable name="BLOCKCLUST_DATA_PATH" action="prepend_to">$INSTALL_DIR/data</environment_variable>
+                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable action="prepend_to" name="BLOCKCLUST_DATA_PATH">$INSTALL_DIR/data</environment_variable>
                 </action>
                 <action type="setup_r_environment">
                     <repository changeset_revision="e16e08f41ed7" name="package_r_3_0_1" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                         <package name="R_3_0_1" version="3.0.1" />
                     </repository>
-                    <repository changeset_revision="54195f1d4b0f" name="'package_samtools_0_1_19" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
-                        <package name="samtools" version="0.1.19 " />
-                    </repository>
                     <r_package>http://cran.r-project.org/src/contrib/ggplot2_0.9.3.1.tar.gz</r_package>
                     <r_package>http://cran.r-project.org/src/contrib/ape_3.0-11.tar.gz</r_package>
                 </action>