Mercurial > repos > big-tiandm > mirplant2

diff tool_dependencies.xml @ 42:3b9a6381e6bf draft

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Uploaded
author big-tiandm
date Tue, 28 Oct 2014 01:35:17 -0400
parents 10df3c84d54a
children 0c4e11018934
line wrap: on
line diff
--- a/tool_dependencies.xml	Tue Oct 28 01:33:17 2014 -0400
+++ b/tool_dependencies.xml	Tue Oct 28 01:35:17 2014 -0400
@@ -1,10 +1,10 @@
 <?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" />
+        <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="http://toolshed.g2.bx.psu.edu" />
+        <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">$REPOSITORY_INSTALL_DIR</environment_variable>
@@ -12,17 +12,22 @@
     <package name="R" version="2.11.0">
         <repository changeset_revision="8d0a55bf7aaf" name="package_r_2_11_0" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" />
     </package>
-	<package name="ViennaRNA" version="2.1.7">
-	   <!--install version="1.0">
+
+	<package name="X11" version="1.5.0">
+		<repositoty name="package_libx11_1_5_0" owner="devteam" />
+	</package>
+
+	<package name="ViennaRNA" version="2.1.8">
+	   <install version="1.0">
 		   <actions>
-		     <action type="download_by_url">http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.7.tar.gz</action>
-			 <action type="shell_command">./configure</action>
+		     <action type="download_by_url">http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.8.tar.gz</action>
+			 <action type="shell_command">./configure --prefix=$INSTALL_DIR </action>
 			 <action type="shell_command">make</action>
 			 <action type="shell_command">make install</action>
 			 <action type="set_environment">
-			   <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+			   <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
 			 </action>
 		   </actions>
-	   </install-->
+	   </install>
 	</package>
 </tool_dependency>