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tool_dependencies.xml
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tool_dependencies.xml
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<?xml version="1.0"?>
<tool_dependency>
<set_environment version="1.0">
<environment_variable action="set_to" name="LINKYX_PATH">$REPOSITORY_INSTALL_DIR</environment_variable>
</set_environment>
<package name="perl" version="5.18.1">
<repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
</package>
<package name="samtools-fpic" version="0.1.19">
<repository changeset_revision="a6c82a5d0b51" name="package_samtools_0_1_19_custom" owner="biomonika" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
</package>
<package name="bioperl" version="1.6.922">
<install version="1.0">
<actions>
<action type="set_environment_for_install">
<repository changeset_revision="a6c82a5d0b51" name="package_samtools_0_1_19_custom" owner="biomonika" toolshed="https://toolshed.g2.bx.psu.edu">
<package name="samtools-fpic" version="0.1.19" />
</repository>
<repository changeset_revision="114b6af405fa" name="package_perl_5_18" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
<package name="perl" version="5.18.1" />
</repository>
</action>
<action type="setup_perl_environment">
<!-- allow downloading and installing an Perl package from cpan.org-->
<package>XML::Parser</package>
<package>http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.6.922.tar.gz</package>
<package>Bio::DB::Fasta</package>
<package>File::Slurp</package>
<package>Bio::DB::Sam</package>
<package>PerlIO::gzip</package>
</action>
</actions>
</install>
<readme>
Bundle::BioPerl
</readme>
</package>
</tool_dependency>