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view tool_dependencies.xml @ 7:fcadce4d9a06 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/bismark commit b'e6ee273f75fff61d1e419283fa8088528cf59470\n'
author bgruening
date Sat, 06 May 2017 13:18:09 -0400
parents 243e8f9fb75b
children
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<?xml version="1.0"?>
<tool_dependency>
	<!-- from test tool shed-->
    <!--<package name="samtools" version="0.1.19">
        <repository changeset_revision="a0ab0fae27e5" name="package_samtools_0_1_19" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu" />
    </package>-->
    <!--from main tool shed-->
    <package name="samtools" version="0.1.19">
        <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="bowtie2" version="2.1.0">
         <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
     </package>
    <!--<package name="bowtie2" version="2.1.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.1.0/bowtie2-2.1.0-source.zip</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                    <source>bowtie2</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bowtie2-align</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>bowtie2-build</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="shell_command">chmod +x $INSTALL_DIR/bin/bowtie2</action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
Compiling bowtie2 requires zlib and libpthread to be present on your system.
        </readme>
    </package>-->
</tool_dependency>