# HG changeset patch
# User bebatut
# Date 1447146325 18000
# Node ID bf5dbe8f7d4ce80a37f2d21bbfe038eb3e1761b9
# Parent  b8ba70feb088689139e509eb8be76394f190d384
planemo upload for repository https://github.com/ASaiM/galaxytools/tree/master/tools/sortmerna/ commit 86b25c80bf4746a0bb73002040487242048a40d2-dirty

diff -r b8ba70feb088 -r bf5dbe8f7d4c sortmerna.xml
--- a/sortmerna.xml	Fri Nov 06 04:40:46 2015 -0500
+++ b/sortmerna.xml	Tue Nov 10 04:05:25 2015 -0500
@@ -11,7 +11,7 @@
 
     <version_command>
 <![CDATA[
-sortmerna --version 2>&1|grep 'SortMeRNA version'
+\${SORTMERNADIR}/sortmerna --version 2>&1|grep 'SortMeRNA version'
 ]]>
     </version_command>
 
@@ -34,11 +34,11 @@
         #end for
     #end if
 
-    indexdb_rna --ref $ref -L $seed_length --max_pos $max_pos
+    \${SORTMERNADIR}/indexdb_rna --ref $ref -L $seed_length --max_pos $max_pos
 
     &&
 
-    sortmerna
+    \${SORTMERNADIR}/sortmerna
         --ref $ref
         --reads $input_sequence_file
         --aligned aligned
diff -r b8ba70feb088 -r bf5dbe8f7d4c tool_dependencies.xml
--- a/tool_dependencies.xml	Fri Nov 06 04:40:46 2015 -0500
+++ b/tool_dependencies.xml	Tue Nov 10 04:05:25 2015 -0500
@@ -5,8 +5,10 @@
             <actions>
                 <action type="download_by_url" target_filename="sortmerna-2.0.tar.gz">https://github.com/biocore/sortmerna/archive/2.0.tar.gz</action>
                 <action type="autoconf"/>
+                <action type="change_directory">../</action>
+                <action type="shell_command">mv sortmerna-2.0/ $INSTALL_DIR/</action>
                 <action type="set_environment">
-                    <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR</environment_variable>
+                    <environment_variable name="SORTMERNADIR" action="set_to">$INSTALL_DIR/sortmerna-2.0/</environment_variable>
                     <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                 </action>
             </actions>