comparison tool_dependencies.xml @ 1:a34ce2b18877

Update tool_dependencies to trinityrnaseq_2013_08_14 and add samtools and bowtie

0:d4ce07eb63bd

<?xml version="1.0"?>
<tool_dependency>
    <package name="trinityrnaseq" version="2013-02-25">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/trinityrnaseq/files/trinityrnaseq_r2013-02-25.tgz</action>
                <action type="shell_command">make</action>
                <action type="move_directory_files">
                    <source_directory>.</source_directory>
                    <destination_directory>$INSTALL_DIR</destination_directory>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
        </readme>
    </package>
</tool_dependency>

1:a34ce2b18877

<?xml version="1.0"?>
<tool_dependency>
    <package name="trinityrnaseq" version="2013_08_14">
        <repository changeset_revision="df23c0ef83a6" name="package_trinityrnaseq_2013_08_14" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="samtools" version="0.1.18">
        <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
    <package name="bowtie" version="1.0.0">
        <repository changeset_revision="e682af6a72cd" name="package_bowtie_1_0_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
    </package>
</tool_dependency>