# HG changeset patch
# User davidvanzessen
# Date 1379944834 14400
# Node ID a5954de04a3d9118512ce39a3edbeddac8c137c7

Uploaded

diff -r 000000000000 -r a5954de04a3d igblastn.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/igblastn.xml	Mon Sep 23 10:00:34 2013 -0400
@@ -0,0 +1,17 @@
+<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 > $output
+    </command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Fasta file"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="text" label="${input.name}-igBLASTn Report"/>
+	<!--<data name="log" format="text" label="log"/>-->
+    </outputs>
+    <help>
+        there is no help
+    </help>
+</tool>
diff -r 000000000000 -r a5954de04a3d tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Mon Sep 23 10:00:34 2013 -0400
@@ -0,0 +1,22 @@
+<?xml version="1.0"?>
+<tool_dependency>
+	<set_environment version="1.0">            
+    </set_environment>
+    
+	<package name="R" version="4.6.3"> 
+        <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="shell_command">tar -zxvf ncbi-igblast-1.0.0-x64-linux.tar.gz</action>
+                
+                <action type="set_environment">
+                	<environment_variable name="IGDATA" action="set_to">$INSTALL_DIR/ncbi-igblast-1.0.0-x64-linux</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>
+			Installs R with apt-get.
+        </readme>
+    </package>
+</tool_dependency>
+