view tool_dependencies.xml @ 22:4e191836de77 default tip

loud perl script

<tool_dependency>
    <set_environment version="1.0">
        <environment_variable name="LINKYX_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>

    <package name="samtools" version="0.1.19">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/samtools/files/samtools/0.1.19/samtools-0.1.19.tar.bz2</action>
                <action type="shell_command">sed -i 's/O2/O2 -fPIC/' Makefile</action>
                <action type="shell_command">make</action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                    <environment_variable name="SAMTOOLS" action="set_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>Compiling samtools with fPIC in order to create bam.h and compiled libbam.a files</readme>
    </package>
    <package name="bioperl" version="1.6.922">
        <install version="1.0">
            <actions>
                <action type="setup_perl_environment">
                    <repository changeset_revision="091a97f8c585" name="package_perl_5_18" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu">
                        <package name="perl" version="5.18.1" />
                    </repository>
                   <!-- 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>
                </action>
            </actions>
        </install>
        <readme>
            Bundle::BioPerl
        </readme>
    </package>
</tool_dependency>