diff tool_dependencies.xml @ 1:7b0d9c107680 draft

Uploaded
author davidvanzessen
date Thu, 23 Jan 2014 08:29:40 -0500
parents d52f6a986108
children
line wrap: on
line diff
--- a/tool_dependencies.xml	Thu Jan 23 08:22:28 2014 -0500
+++ b/tool_dependencies.xml	Thu Jan 23 08:29:40 2014 -0500
@@ -6,35 +6,15 @@
 	<package name="igBlastn" version="1.0.0"> 
         <install version="1.0">
             <actions>
-            	<action type="download_by_url" target_filename="ncbi-igblast-1.0.0-x64-linux.tar.gz">
-            		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_directory_files">
-		    		<source_directory>ncbi-igblast-1.0.0</source_directory>
-			   		<destination_directory>$INSTALL_DIR/ncbi-igblast-1.0.0</destination_directory>
-	       		</action>
-                <action type="set_environment">
-                	<environment_variable name="IGDATA" action="set_to">$INSTALL_DIR/ncbi-igblast-1.0.0</environment_variable>
-                </action>
+            	<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>
-
-                <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>
+</tool_dependency>
\ No newline at end of file