diff tool_dependencies.xml @ 1:533b3b2a1e66 draft default tip

Update Orione citation. Add <citations> tag. Use package_muscle_3_8_31 from iuc.

--- a/tool_dependencies.xml	Wed Oct 30 07:34:04 2013 -0400
+++ b/tool_dependencies.xml	Thu Jun 04 11:34:04 2015 -0400
@@ -1,27 +1,11 @@
 <?xml version="1.0"?>
 <tool_dependency>
+  <set_environment version="1.0">
+    <!-- MUSCLE may require a lot of memory and computation time for a medium/large input multi-FASTA file, therefore a limit on the file size is enforced by the tool.
+Change the FASTA_MAX_SIZE variable in the installed env.sh file to adjust this limit to your needs and available resources. -->
+    <environment_variable action="set_to" name="FASTA_MAX_SIZE">100000</environment_variable>
+  </set_environment>
   <package name="muscle" version="3.8.31">
-    <install version="1.0">
-      <actions>
-        <action type="download_by_url" target_filename="muscle3.8.31.tar.gz">http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_src.tar.gz</action>
-        <!-- When compiling, need to remove the '-static' linker option from the src/mk file used by src/Makefile -->
-        <action type="shell_command">sed -i 's/-static//g' src/mk</action>
-        <action type="shell_command">make -C src/</action>
-        <action type="move_file">
-          <source>src/muscle</source>
-          <destination>$INSTALL_DIR/bin</destination>
-        </action>
-        <action type="set_environment">
-          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
-        </action>
-        <action type="set_environment">
-          <environment_variable name="FASTA_MAX_SIZE" action="set_to">100000</environment_variable>
-        </action>
-      </actions>
-    </install>
-    <readme>
-MUSCLE may require a lot of memory and computation time for a medium/large input multi-FASTA file, therefore a limit on the file size is enforced by the tool.
-Change the FASTA_MAX_SIZE variable in the installed env.sh file to adjust this limit to your needs and available resources.
-    </readme>
+    <repository changeset_revision="8f20b47725d8" name="package_muscle_3_8_31" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
   </package>
 </tool_dependency>