Mercurial > repos > davidvanzessen > igblast_human

changeset 2:40954f0f8d14 draft

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Uploaded
author davidvanzessen
date Tue, 24 Sep 2013 04:01:28 -0400
parents 0ccde52e24a1
children 65f8bb1b0701
files igblastn.xml tool_dependencies.xml
diffstat 2 files changed, 4 insertions(+), 1 deletions(-) [+]
line wrap: on
line diff
--- a/igblastn.xml	Mon Sep 23 10:03:38 2013 -0400
+++ b/igblastn.xml	Tue Sep 24 04:01:28 2013 -0400
@@ -1,7 +1,6 @@
 <tool id="igblastn" name="igBLASTn" version="0.1.0">
     <description>Run igBLASTn</description>
     <command>
-    export IGDATA=/usr/local/ncbi-igblast-1.0.0/;
     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 > $output
     </command>
     <inputs>
--- a/tool_dependencies.xml	Mon Sep 23 10:03:38 2013 -0400
+++ b/tool_dependencies.xml	Tue Sep 24 04:01:28 2013 -0400
@@ -7,6 +7,10 @@
         <install version="1.0">
             <actions>
             	<action type="download_by_url">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.0.0/ncbi-igblast-1.0.0-x64-linux.tar.gz</action>
+            	<action type="move_file">
+            		<source>ncbi-igblast-1.0.0-x64-linux.tar.gz</source>
+            		<destination>$INSTALL_DIR</destination>
+            	</action>
                 <action type="shell_command">tar -zxvf ncbi-igblast-1.0.0-x64-linux.tar.gz</action>
                 
                 <action type="set_environment">