# HG changeset patch
# User iuc
# Date 1437157117 14400
# Node ID a3c3535a61a5f152bda617e9a967cb3c107ad1c3
# Parent  a3fb2752c3409e7e40078f1b53056999e62e4c07
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trnascan_1_3_1 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty

diff -r a3fb2752c340 -r a3c3535a61a5 tool_dependencies.xml
--- a/tool_dependencies.xml	Tue Feb 25 12:34:44 2014 -0500
+++ b/tool_dependencies.xml	Fri Jul 17 14:18:37 2015 -0400
@@ -7,12 +7,13 @@
                 <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">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">rm Makefile &amp;&amp; mv Makefile_new Makefile</action>
+                <action type="shell_command">sed -i.bak -e "s|^BINDIR  = .*|BINDIR = $INSTALL_DIR/bin/|" Makefile</action>
+                <action type="shell_command">sed -i.bak -e "s|^LIBDIR  = .*|LIBDIR = $INSTALL_DIR/lib/tRNAscan-SE/|" Makefile</action>
+                <action type="shell_command">sed -i.bak -e "s|^MANDIR  = .*|MANDIR = $INSTALL_DIR/man|" Makefile</action>
                 <action type="make_install"/>
 
                 <!-- 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="download_file">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">