Mercurial > repos > malbuquerque > factera

diff factera/tool_dependencies.xml @ 30:12c14221b302 draft default tip

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author malbuquerque
date Fri, 16 Jan 2015 20:15:33 -0500
parents 9770263a050c
children
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/factera/tool_dependencies.xml	Fri Jan 16 20:15:33 2015 -0500
@@ -0,0 +1,45 @@
+<?xml version="1.0"?>
+<tool_dependency>
+  
+	<package name="blast+" 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="samtools" 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="310">		
+		<repository changeset_revision="f945f71702cc" name="package_ucsc_user_apps_310" owner="malbuquerque" toolshed="https://toolshed.g2.bx.psu.edu" />
+	</package>
+
+	<package name="perl_descriptive_statistics" version="3.0608">
+		<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="factera" 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>