Mercurial > repos > bigrna > gpsrna
diff tool_dependencies.xml @ 0:87fe81de0931 draft default tip
Uploaded
| author | bigrna |
|---|---|
| date | Sun, 04 Jan 2015 02:47:25 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tool_dependencies.xml Sun Jan 04 02:47:25 2015 -0500 @@ -0,0 +1,134 @@ +<?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>