Mercurial > repos > jeremie > package_breakdancer_1_2_6

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author jeremie
date Tue, 01 Jul 2014 11:06:05 -0400
parents 1c615a6bb33d
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<?xml version="1.0"?>
<tool_dependency>
    <package name="breakdancer" version="1.2.6">
        <install version="1.0">
            <actions_group>
            <!--     <actions architecture="i386" os="linux">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/freebayes/freebayes-0.9.6_9608597d-Linux-i686.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>       
                </actions>     -->            
                <actions>
                    <action type="shell_command">git clone --recursive https://github.com/genome/breakdancer</action>
                    <!-- <action type="download_by_url">https://github.com/genome/breakdancer/archive/master.zip</action> -->
                    <action type="shell_command">mkdir build</action>
                    <action type="change_directory">build</action>
                    <action type="shell_command">cmake .. -DCMAKE_BUILD_TYPE=release -DCMAKE_INSTALL_PREFIX=/usr/local</action>
                    <action type="shell_command">make</action>
                    <action type="move_file">
                        <source>bin/breakdancer-max</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>../perl/bam2cfg.pl</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>../perl/AlnParser.pm</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <!-- <action type="download_by_url">http://9ypffrj86h.1fichier.com/breakdancer2vcf.py</action> -->
                    <action type="shell_command">wget https://raw.githubusercontent.com/ALLBio/allbiotc2/master/breakdancer/breakdancer2vcf.py</action>
                    <action type="move_file">
                        <source>breakdancer2vcf.py</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <!-- <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>    -->   
                    <action type="set_environment">
                        <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    </action>
                    <action type="set_environment">
                        <environment_variable name="BREAKDANCER_BIN" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    </action>
                </actions>                     
            </actions_group>
        </install>
        <readme>
        </readme>
    </package>
</tool_dependency>