Mercurial > repos > davidvanzessen > combined_immune_repertoire_pipeline

diff tool_dependencies.xml @ 0:4e3df2384422 draft

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author davidvanzessen
date Wed, 20 Nov 2013 10:00:28 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Nov 20 10:00:28 2013 -0500
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+<?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="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="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/
+        </readme>
+    </package>
+</tool_dependency>