Mercurial > repos > big-tiandm > mirplant2

diff tool_dependencies.xml @ 49:f008ab2cadc6 draft

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author big-tiandm
date Wed, 03 Dec 2014 02:03:27 -0500
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children 7b5a48b972e9
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Wed Dec 03 02:03:27 2014 -0500
@@ -0,0 +1,48 @@
+<?xml version="1.0"?>
+<tool_dependency>
+    <package name="fastx_toolkit" version="0.0.13">
+        <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <package name="bowtie" version="0.12.7">
+        <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+    </package>
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+	<!--package name="R" version="3.0.1">
+	   <repository name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" />
+	</package!-->
+
+	<package name="ViennaRNA" version="2.1.8">
+	   <install version="1.0">
+		   <actions>
+		     <action type="download_by_url">http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.8.tar.gz</action>
+			 <action type="shell_command">./configure --prefix=$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="PATH">$INSTALL_DIR/bin</environment_variable>
+			 </action>
+		   </actions>
+	   </install>
+	</package>
+
+	<package name="SVG" version="2.59">
+	   <install version="1.0">
+		   <actions>
+		     <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/SVG-2.59.tar.gz</action>
+			<action type="make_directory">$INSTALL_DIR/lib/perl5</action>
+			<action type="shell_command">
+				perl Makefile.PL INSTALL_BASE=$INSTALL_DIR &amp;&amp;
+				make &amp;&amp;
+				make install 
+			</action>
+			<action type="set_environment">
+				<environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable>	
+			</action>
+		   </actions>
+	   </install>
+	</package>
+
+
+</tool_dependency>