# HG changeset patch
# User davidvanzessen
# Date 1390473359 18000
# Node ID 99541760fdfe99f5ba107a7bb6e4a1d9a9330dd9
# Parent  ddc765e7142cf3eae8579dd8b95d5ad26e252256
Uploaded

diff -r ddc765e7142c -r 99541760fdfe database.zip
diff -r ddc765e7142c -r 99541760fdfe igblastn.sh
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/igblastn.sh	Thu Jan 23 05:35:59 2014 -0500
@@ -0,0 +1,7 @@
+dir="$(cd "$(dirname "$0")" && pwd)"
+echo "dir = $dir"
+echo "pwd = $PWD"
+mkdir $PWD/igblastdatabase
+unzip $dir/database.zip -d $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
diff -r ddc765e7142c -r 99541760fdfe igblastn.xml
--- a/igblastn.xml	Tue Dec 03 04:33:59 2013 -0500
+++ b/igblastn.xml	Thu Jan 23 05:35:59 2014 -0500
@@ -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
+    <command interpreter="bash">
+		igblastn.sh $input $output
     </command>
     <inputs>
         <param name="input" type="data" format="fasta" label="Fasta file"/>
diff -r ddc765e7142c -r 99541760fdfe tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Dec 03 04:33:59 2013 -0500
+++ b/tool_dependencies.xml	Thu Jan 23 05:35:59 2014 -0500
@@ -21,20 +21,10 @@
                 <action type="set_environment">
                 	<environment_variable name="PATH" action="prepend_to">$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>
-                                
-                <action type="shell_command">wget -r -np -nH --cut-dirs=4 -R index.html -P $INSTALL_DIR/ncbi-igblast-1.0.0 "ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data"</action>
-                
-                <action type="shell_command">wget -r -np -nH --cut-dirs=4 -R index.html -P $INSTALL_DIR/ncbi-igblast-1.0.0 "ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/database"</action>
-                
-                <action type="shell_command">wget -r -np -nH --cut-dirs=4 -R index.html -P $INSTALL_DIR/ncbi-igblast-1.0.0 "ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/optional_file"</action>
-            	
             </actions>
         </install>
         <readme>
-		Downloads igBlast with the latest database provided by NCBI, output may change depending on the database available at ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/
+			Downloads the igblastn-1.0.0 executable from NCBI and uses a fixed database included in this tool.
         </readme>
     </package>
 </tool_dependency>