Mercurial > repos > bigrna > gpsrna
view tool_dependencies.xml @ 0:87fe81de0931 draft default tip
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author | bigrna |
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date | Sun, 04 Jan 2015 02:47:25 -0500 |
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<?xml version="1.0"?> <tool_dependency> <package name="fastx_toolkit" version="0.0.13"> <repository changeset_revision="ec66ae4c269b" name="package_fastx_toolkit_0_0_13" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <package name="bowtie" version="0.12.7"> <repository changeset_revision="9f9f38617a98" name="package_bowtie_0_12_7" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> </package> <set_environment version="1.0"> <environment_variable action="set_to" name="SCRIPT_PATH">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> <!--package name="R" version="3.0.1"> <repository name="package_r_3_0_1" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> </package!--> <package name="ViennaRNA" version="2.1.8"> <install version="1.0"> <actions> <action type="download_by_url">http://www.tbi.univie.ac.at/RNA/packages/source/ViennaRNA-2.1.8.tar.gz</action> <action type="shell_command">./configure --prefix=$INSTALL_DIR </action> <action type="shell_command">make</action> <action type="shell_command">make install</action> <action type="set_environment"> <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> </package> <package name="R" version="3.0.1"> <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu" /> <install version="1.0"> <actions> <action type="set_environment_for_install"> <repository changeset_revision="c5ff6dd33c79" name="package_r_3_0_1" owner="iuc" prior_installation_required="True" toolshed="http://toolshed.g2.bx.psu.edu"> <package name="R" version="3.0.1" /> </repository> </action> <action type="shell_command">R CMD BATCH $REPOSITORY_INSTALL_DIR/install_DEG.R </action> <action type="shell_command">echo "export PATH=$PATH" > $INSTALL_DIR/env.sh </action> <action type="shell_command">chmod 755 $INSTALL_DIR/env.sh </action> </actions> </install> </package> <package name="threads" version="1.96"> <install version="1.0"> <actions> <action type="download_by_url">http://www.cpan.org/authors/id/J/JD/JDHEDDEN/threads-1.96.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/perl5</action> <action type="shell_command"> perl Makefile.PL INSTALL_BASE=$INSTALL_DIR && make && make install </action> <action type="set_environment"> <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable> </action> </actions> </install> </package> <package name="Parallel-ForkManager" version="1.06"> <install version="1.0"> <actions> <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/Parallel-ForkManager-1.06.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/perl5</action> <action type="shell_command"> perl Makefile.PL INSTALL_BASE=$INSTALL_DIR && make && make install </action> <action type="set_environment"> <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable> </action> </actions> </install> </package> <package name="Boost-Graph" version="1.4_001"> <install version="1.0"> <actions> <action type="download_by_url">http://www.cpan.org/authors/id/D/DU/DUFFEE/Boost-Graph-1.4_001.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/perl5</action> <action type="shell_command"> perl Makefile.PL INSTALL_BASE=$INSTALL_DIR && ls && make && make install </action> <action type="set_environment"> <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable> </action> </actions> </install> </package> <package name="SVG" version="2.59"> <install version="1.0"> <actions> <action type="download_by_url">http://www.cpan.org/authors/id/S/SZ/SZABGAB/SVG-2.59.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/perl5</action> <action type="shell_command"> perl Makefile.PL INSTALL_BASE=$INSTALL_DIR && make && make install </action> <action type="set_environment"> <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable> </action> </actions> </install> </package> <!--package name="parent" version="0.228"> <install version="1.0"> <actions> <action type="download_by_url">http://www.cpan.org/authors/id/C/CO/CORION/parent-0.228.tar.gz</action> <action type="make_directory">$INSTALL_DIR/lib/perl5</action> <action type="shell_command"> perl Makefile.PL INSTALL_BASE=$INSTALL_DIR && make && make install </action> <action type="set_environment"> <environment_variable action="append_to" name="PERL5LIB">$INSTALL_DIR/lib/perl5/:$INSTALL_DIR/lib/perl5/x86_64-linux-gnu-thread-multi/</environment_variable> </action> </actions> </install> </package--> </tool_dependency>