Mercurial > repos > davidvanzessen > igblast_human

changeset 42:46fbf2f2d1aa draft

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Uploaded
author davidvanzessen
date Thu, 26 Sep 2013 10:26:59 -0400
parents 12de5aa44543
children 1c64c977624e
files igblastn.xml tool_dependencies.xml
diffstat 2 files changed, 4 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- 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 > $output
     </command>
     <inputs>
         <param name="input" type="data" format="fasta" label="Fasta file"/>
--- a/tool_dependencies.xml	Thu Sep 26 06:54:02 2013 -0400
+++ b/tool_dependencies.xml	Thu Sep 26 10:26:59 2013 -0400
@@ -18,6 +18,9 @@
                 <action type="set_environment">
                 	<environment_variable name="IGDATA" action="set_to">$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>