Mercurial > repos > malbuquerque > factera

diff factera/tool_dependencies.xml @ 4:bcee925a2db9 draft

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author malbuquerque
date Thu, 15 Jan 2015 20:17:00 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/factera/tool_dependencies.xml	Thu Jan 15 20:17:00 2015 -0500
@@ -0,0 +1,52 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  
+	<package name="blast_plus_blast_plus_2_2_26" version="2.2.26">
+    <repository changeset_revision="85e43fb3f363" name="package_blast_plus_2_2_26" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+
+	<package name="package_samtools_0_1_19" version="0.1.19">
+		<repository changeset_revision="95d2c4aefb5f" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+	</package>
+
+	<package name="ucsc_user_apps" version="1.0.0">		
+		<repository changeset_revision="7d36c043e340" name="ucsc_user_apps" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu" />
+	</package>
+
+	<package name="factera_perl_dependency" version="1.4.3">
+		<install version="1.0">
+			<actions>
+
+				<action type="download_by_url">http://search.cpan.org/CPAN/authors/id/S/SH/SHLOMIF/Statistics-Descriptive-3.0608.tar.gz</action>
+				<action type="shell_command">perl Makefile.PL PREFIX=$INSTALL_DIR</action>
+				<action type="shell_command">make</action>
+				<action type="shell_command">make install</action>
+				
+				<action type="set_environment">
+					<environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/site_perl</environment_variable>
+				</action>
+
+			</actions>
+		</install>	
+	</package>
+
+	<package name="package_factera_1_4_3" version="1.4.3">
+		<install version="1.0">
+  		<actions>
+				
+      	<action type="download_by_url">http://factera.stanford.edu/files/factera-v1.4.3.pl</action>
+        
+				<action type="move_directory_files">
+					<source_directory>.</source_directory>
+					<destination_directory>$INSTALL_DIR</destination_directory>
+				</action>
+
+				<action type="set_environment">
+					<environment_variable action="set_to" name="FACTERA_DIR">$INSTALL_DIR</environment_variable>
+				</action>
+
+			</actions>
+		</install>
+	</package>
+
+</tool_dependency>