# HG changeset patch
# User iuc
# Date 1378638835 14400
# Node ID 2ddcff5d0fa2ca208a5ef52c73037a2ae8f34143

Uploaded

diff -r 000000000000 -r 2ddcff5d0fa2 tool_dependencies.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml	Sun Sep 08 07:13:55 2013 -0400
@@ -0,0 +1,26 @@
+<tool_dependency>
+    <package name="tRNAscan-SE" version="1.3.1">
+        <install version="1.0">
+            <actions>
+                <action type="download_by_url">http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz</action>
+                <action type="make_directory">$INSTALL_DIR/bin/</action>
+                <action type="make_directory">$INSTALL_DIR/lib/tRNAscan-SE/</action>
+                <action type="make_directory">$INSTALL_DIR/man/</action>
+                <!-- replacing the hardcoded pathvariables with the real ones -->
+                <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; sed 's%^BINDIR  = .*%BINDIR = $INSTALL_DIR/bin/%' Makefile | sed 's%^LIBDIR  = .*%LIBDIR = $INSTALL_DIR/lib/tRNAscan-SE/%' | sed 's%^MANDIR  = .*%MANDIR = $INSTALL_DIR/man%' > Makefile_new</action>
+                <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; rm Makefile &amp;&amp; mv Makefile_new Makefile</action>
+                <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; make &amp;&amp; make install</action>
+
+                <!-- for some reason infernal needs to be directly under the bin/ from tRNAScan -->
+                <action type="shell_command">wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action>
+                <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action>
+                <action type="shell_command">cd infernal-1.0.2 &amp;&amp; ./configure --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install</action>
+                <action type="set_environment">
+                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+                    <environment_variable name="PERL5LIB" action="prepend_to">$INSTALL_DIR/bin/</environment_variable>
+                </action>
+            </actions>
+        </install>
+        <readme>Compiling and running tRNAScan-SE requires gcc a PERL environment.</readme>
+    </package>
+</tool_dependency>