# HG changeset patch
# User davidvanzessen
# Date 1380033751 14400
# Node ID 215aa111db641aa0a10487a0320f56c66ffaaba2
# Parent  1d15cd0bd9131bac55f057649c9a6ceb03b681a5
Uploaded

diff -r 1d15cd0bd913 -r 215aa111db64 igblastn.xml
--- 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"/>
diff -r 1d15cd0bd913 -r 215aa111db64 igblastn.xml~
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/igblastn.xml~	Tue Sep 24 10:42:31 2013 -0400
@@ -0,0 +1,19 @@
+<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 > $output
+    </command>
+    <inputs>
+        <param name="input" type="data" format="fasta" label="Fasta file"/>
+    </inputs>
+    <outputs>
+        <data name="output" format="text" label="${input.name}-igBLASTn Report"/>
+	<!--<data name="log" format="text" label="log"/>-->
+    </outputs>
+	<requirements>
+		<requirement type="package" version="1.0.0">igBlastn</requirement>
+	</requirements>
+    <help>
+        there is no help
+    </help>
+</tool>
diff -r 1d15cd0bd913 -r 215aa111db64 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Sep 24 10:15:19 2013 -0400
+++ b/tool_dependencies.xml	Tue Sep 24 10:42:31 2013 -0400
@@ -18,167 +18,16 @@
                 <action type="set_environment">
                 	<environment_variable name="IGDATA" action="set_to">$INSTALL_DIR/ncbi-igblast-1.0.0</environment_variable>
                 </action>
-                
-                <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human.ndm.imgt</action>
-                <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human.ndm.kabat</action>
-                <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human.pdm.imgt</action>
-                <action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human.pdm.kabat</action>
-
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nhr</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nin</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nog</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nsd</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nsi</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.nsq</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.phr</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.pin</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.pog</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.psd</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.psi</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_TR_V.psq</action>
-                
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nhr</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nin</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nog</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nsd</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nsi</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.nsq</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.phr</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.pin</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.pog</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.psd</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.psi</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V.psq</action>
-				<action type="download_file">ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data/human/human_V_prot</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="move_file">
-				    <source>human_V</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_V.nhr</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_V.nin</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_V.nog</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_V.nsd</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_V.nsi</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_V.nsq</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_V.phr</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_V.pin</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_V.pog</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_V.psd</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_V.psi</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_V.psq</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_V_prot</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-
-
-                <action type="move_file">
-				    <source>human.ndm.imgt</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human.ndm.kabat</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human.pdm.imgt</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human.pdm.kabat</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-
-                <action type="move_file">
-				    <source>human_TR_V.nhr</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_TR_V.nin</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_TR_V.nog</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_TR_V.nsd</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_TR_V.nsi</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_TR_V.nsq</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_TR_V.phr</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_TR_V.pin</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_TR_V.pog</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_TR_V.psd</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_TR_V.psi</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-                <action type="move_file">
-				    <source>human_TR_V.psq</source>
-				    <destination>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data/human</destination>
-                </action>
-
+                                
+                <action type="shell_command">wget -r -np -nH --cut-dirs=4 -R index.html -P $INSTALL_DIR/internal_data "ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data"</action>
+            	<action type="move_directory_files">
+            		<source_directory>internal_data</source_directory>
+            		<destination_directory>$INSTALL_DIR/ncbi-igblast-1.0.0/internal_data</destination_directory>
+            	</action>
+            	
             </actions>
         </install>
         <readme>