Mercurial > repos > big-tiandm > mirplant2

diff tool_dependencies.xml @ 20:d88fc3c0084e draft

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author big-tiandm
date Fri, 25 Jul 2014 05:32:24 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Fri Jul 25 05:32:24 2014 -0400
@@ -0,0 +1,28 @@
+<?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="http://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="http://toolshed.g2.bx.psu.edu" />
+    </package>
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
+    <package name="R" version="2.11.0">
+        <repository changeset_revision="8d0a55bf7aaf" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
+    </package>
+	<package name="ViennaRNA" version="1.5">
+	   <install version="1.0">
+		   <actions>
+		     <action type="download_by_url">http://web.mit.edu/seven/src/ViennaRNA-1.5beta.tar.gz</action>
+			 <action type="shell_command">./configure --prefix=$INSTALL_DIR --datadir=$INSTALL_DIR</action>
+			 <action type="shell_command">make</action>
+			 <action type="shell_command">make install</action>
+			 <action type="set_environment">
+			   <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
+			 </action>
+		   </actions>
+	   </install>
+	</package>
+</tool_dependency>