Mercurial > repos > davidvanzessen > igblast_human

diff igblastn.xml @ 37:215aa111db64 draft

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Uploaded
author davidvanzessen
date Tue, 24 Sep 2013 10:42:31 -0400
parents 40954f0f8d14
children 46fbf2f2d1aa
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--- a/igblastn.xml	Tue Sep 24 10:15:19 2013 -0400
+++ b/igblastn.xml	Tue Sep 24 10:42:31 2013 -0400
@@ -1,7 +1,7 @@
 <tool id="igblastn" name="igBLASTn" version="0.1.0">
     <description>Run igBLASTn</description>
     <command>
-    igblastn -germline_db_V /usr/local/ncbi-igblast-1.0.0/database/human_gl_V -germline_db_J /usr/local/ncbi-igblast-1.0.0/database/human_gl_J -germline_db_D /usr/local/ncbi-igblast-1.0.0/database/human_gl_D -domain_system imgt -query $input -auxiliary_data /usr/local/ncbi-igblast-1.0.0/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"/>