--- a/tool_dependencies.xml	Sat Jul 06 10:37:13 2013 -0400
+++ b/tool_dependencies.xml	Thu Jan 22 13:15:51 2015 -0500
@@ -1,47 +1,15 @@
 <?xml version="1.0"?>
 <tool_dependency>
     <package name="biopython" version="1.61">
-        <repository changeset_revision="5d0c54f7fea2" name="package_biopython_1_61" owner="biopython" toolshed="http://toolshed.g2.bx.psu.edu" />
+        <repository changeset_revision="ae9dda584395" name="package_biopython_1_61" owner="biopython" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="aragorn" version="1.2.36">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://mbio-serv2.mbioekol.lu.se/ARAGORN/Downloads/aragorn1.2.36.tgz</action>
-                <action type="make_directory">$INSTALL_DIR/bin/</action>
-                <action type="shell_command">gcc -O3 -ffast-math -finline-functions -o aragorn aragorn1.2.36.c</action>
-                <action type="move_file">
-                    <source>aragorn</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>Compiling ARAGORN requires gcc.</readme>
+        <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
     <package name="tRNAscan-SE" version="1.3.1">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz</action>
-                <action type="make_directory">$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 = $INSTALL_DIR/man%' &gt; Makefile_new</action>
-                <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; rm Makefile &amp;&amp; mv Makefile_new Makefile</action>
-                <action type="shell_command">cd ./tRNAscan-SE-1.3.1 &amp;&amp; make &amp;&amp; make install</action>
-
-                <!-- for some reason infernal needs to be directly under the bin/ from tRNAScan -->
-                <action type="shell_command">wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action>
-                <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action>
-                <action type="shell_command">cd infernal-1.0.2 &amp;&amp; ./configure --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install</action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                    <environment_variable action="prepend_to" name="PERL5LIB">$INSTALL_DIR/bin/</environment_variable>
-                </action>
-            </actions>
-        </install>
-        <readme>Compiling and running tRNAScan-SE requires gcc a PERL environment.</readme>
+        <repository changeset_revision="a3fb2752c340" name="package_trnascan_1_3_1" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
+    <set_environment version="1.0">
+        <environment_variable action="set_to" name="TRNAPRED_SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
+    </set_environment>
 </tool_dependency>