# HG changeset patch
# User davidvanzessen
# Date 1380205619 14400
# Node ID 46fbf2f2d1aae2118c935730939218f293755435
# Parent  12de5aa44543841a59f59fffb63d508cc9892849
Uploaded

diff -r 12de5aa44543 -r 46fbf2f2d1aa igblastn.xml
--- a/igblastn.xml	Thu Sep 26 06:54:02 2013 -0400
+++ b/igblastn.xml	Thu Sep 26 10:26:59 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="igblastn" name="igBLASTn" version="0.1.0">
     <description>Run igBLASTn</description>
     <command>
-    igblastn -germline_db_V \$IGDATA/database/human_gl_V -germline_db_J \$IGDATA/database/human_gl_J -germline_db_D \$IGDATA/database/human_gl_D -domain_system imgt -query $input -auxiliary_data \$IGDATA/optional_file/human_gl.aux -show_translation -outfmt 3 > $output
+		igblastn -germline_db_V \$IGDATA/database/human_gl_V -germline_db_J \$IGDATA/database/human_gl_J -germline_db_D \$IGDATA/database/human_gl_D -domain_system imgt -query $input -auxiliary_data \$IGDATA/optional_file/human_gl.aux -show_translation -outfmt 3 > $output
     </command>
     <inputs>
         <param name="input" type="data" format="fasta" label="Fasta file"/>
diff -r 12de5aa44543 -r 46fbf2f2d1aa tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Sep 26 06:54:02 2013 -0400
+++ b/tool_dependencies.xml	Thu Sep 26 10:26:59 2013 -0400
@@ -18,6 +18,9 @@
                 <action type="set_environment">
                 	<environment_variable name="IGDATA" action="set_to">$INSTALL_DIR/ncbi-igblast-1.0.0</environment_variable>
                 </action>
+                <action type="set_environment">
+                	<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/ncbi-igblast-1.0.0/bin</environment_variable>
+                </action>
 
                 <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data</action>
                 <action type="make_directory">$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</action>