# HG changeset patch
# User davidvanzessen
# Date 1408543449 14400
# Node ID a700a552f031662591ce4a0d3053e92b4e23e91c
# Parent  39a916965683b91dd26cdf13b5377cf2a7527882
Uploaded

diff -r 39a916965683 -r a700a552f031 databasenew.zip
Binary file databasenew.zip has changed
diff -r 39a916965683 -r a700a552f031 igblastn.sh
--- a/igblastn.sh	Thu Jan 23 08:32:42 2014 -0500
+++ b/igblastn.sh	Wed Aug 20 10:04:09 2014 -0400
@@ -1,9 +1,7 @@
 dir="$(cd "$(dirname "$0")" && pwd)"
-echo "dir = $dir"
-echo "pwd = $PWD"
 mkdir $PWD/igblastdatabase
 unzip $dir/database.zip -d $PWD/igblastdatabase/
 
 export IGDATA=$PWD/igblastdatabase/
 
-igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $2
+/home/galaxy/galaxy/igblast/igblastn -germline_db_V $PWD/igblastdatabase/database/human_gl_V -germline_db_J $PWD/igblastdatabase/database/human_gl_J -germline_db_D $PWD/igblastdatabase/database/human_gl_D -domain_system imgt -query $1 -auxiliary_data $PWD/igblastdatabase/optional_file/human_gl.aux -show_translation -outfmt 3 > $2
diff -r 39a916965683 -r a700a552f031 igblastn.xml
--- a/igblastn.xml	Thu Jan 23 08:32:42 2014 -0500
+++ b/igblastn.xml	Wed Aug 20 10:04:09 2014 -0400
@@ -10,9 +10,6 @@
         <data name="output" format="text" label="${input.name}-igBLASTn Report"/>
 	<!--<data name="log" format="text" label="log"/>-->
     </outputs>
-	<requirements>
-		<requirement type="package" version="1.0.0">igBlastn</requirement>
-	</requirements>
     <help>
         Step 1 of the Immune Repertoire tools, generates a report to be parsed with the "igparse" tool.
     </help>
diff -r 39a916965683 -r a700a552f031 tool_dependencies.xml
--- a/tool_dependencies.xml	Thu Jan 23 08:32:42 2014 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-<?xml version="1.0"?>
-<tool_dependency>
-	<set_environment version="1.0">            
-    </set_environment>
-    
-	<package name="igBlastn" version="1.0.0"> 
-        <install version="1.0">
-            <actions>
-            	<action type="shell_command">wget ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.0.0/ncbi-igblast-1.0.0-x64-linux.tar.gz -P $INSTALL_DIR</action>
-            	<action type="shell_command">tar zxvf $INSTALL_DIR/ncbi-igblast-1.0.0-x64-linux.tar.gz -C $INSTALL_DIR</action>
-                <action type="set_environment">
-                	<environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/ncbi-igblast-1.0.0/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>
-			Downloads the igblastn-1.0.0 executable from NCBI and uses a fixed database included in this tool.
-        </readme>
-    </package>
-</tool_dependency>