Mercurial > repos > iuc > package_trnascan_1_3_1

comparison tool_dependencies.xml @ 2:a3c3535a61a5 draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trnascan_1_3_1 commit 025696892784ba9fd07404ce4d21f3dca4ac1a1e-dirty
author iuc
date Fri, 17 Jul 2015 14:18:37 -0400
parents a3fb2752c340
children
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1:a3fb2752c340 2:a3c3535a61a5
5 <action type="download_by_url">http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz</action> 5 <action type="download_by_url">http://lowelab.ucsc.edu/software/tRNAscan-SE.tar.gz</action>
6 <action type="make_directory">$INSTALL_DIR/bin/</action> 6 <action type="make_directory">$INSTALL_DIR/bin/</action>
7 <action type="make_directory">$INSTALL_DIR/lib/tRNAscan-SE/</action> 7 <action type="make_directory">$INSTALL_DIR/lib/tRNAscan-SE/</action>
8 <action type="make_directory">$INSTALL_DIR/man/</action> 8 <action type="make_directory">$INSTALL_DIR/man/</action>
9 <!-- replacing the hardcoded pathvariables with the real ones --> 9 <!-- replacing the hardcoded pathvariables with the real ones -->
10 <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> 10 <action type="shell_command">sed -i.bak -e "s|^BINDIR = .*|BINDIR = $INSTALL_DIR/bin/|" Makefile</action>
11 <action type="shell_command">rm Makefile &amp;&amp; mv Makefile_new Makefile</action> 11 <action type="shell_command">sed -i.bak -e "s|^LIBDIR = .*|LIBDIR = $INSTALL_DIR/lib/tRNAscan-SE/|" Makefile</action>
12 <action type="shell_command">sed -i.bak -e "s|^MANDIR = .*|MANDIR = $INSTALL_DIR/man|" Makefile</action>
12 <action type="make_install"/> 13 <action type="make_install"/>
13 14
14 <!-- for some reason infernal needs to be directly under the bin/ from tRNAScan --> 15 <!-- for some reason infernal needs to be directly under the bin/ from tRNAScan -->
15 <action type="shell_command">wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action> 16 <action type="download_file">ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz</action>
16 <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action> 17 <action type="shell_command">tar xfvz infernal-1.0.2.tar.gz</action>
17 <action type="shell_command">cd infernal-1.0.2 &amp;&amp; ./configure --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install</action> 18 <action type="shell_command">cd infernal-1.0.2 &amp;&amp; ./configure --prefix=$INSTALL_DIR &amp;&amp; make &amp;&amp; make install</action>
18 <action type="set_environment"> 19 <action type="set_environment">
19 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> 20 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
20 <environment_variable name="PERL5LIB" action="prepend_to">$INSTALL_DIR/bin/</environment_variable> 21 <environment_variable name="PERL5LIB" action="prepend_to">$INSTALL_DIR/bin/</environment_variable>