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Add extract_splice_sites.py for converting GTF files
author Jim Johnson <jj@umn.edu>
date Fri, 25 Jul 2014 11:13:18 -0500
parents 53ed3caf1d9d
children
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<?xml version="1.0"?>
<tool_dependency>
    <package name="hisat" version="0.1.0-beta">
        <install version="1.0">
            <actions_group>
                <actions architecture="x86_64" os="linux">
                    <action type="download_by_url">http://ccb.jhu.edu/software/hisat/downloads/hisat-0.1.0-beta-Linux_x86_64.zip</action>
                    <action type="move_file">
                        <source>hisat</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>hisat-align</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>hisat-build</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>hisat-inspect</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>extract_splice_sites.py</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                </actions>
                <actions architecture="x86_64" os="darwin">
                    <action type="download_by_url">http://ccb.jhu.edu/software/hisat/downloads/hisat-0.1.0-beta-OSX_x86_64.zip</action>
                    <action type="move_file">
                        <source>hisat</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>hisat-align</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>hisat-build</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>hisat-inspect</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>extract_splice_sites.py</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                </actions>
                <actions>
                    <action type="download_by_url">http://ccb.jhu.edu/software/hisat/downloads/hisat-0.1.0-beta-source.zip</action>
                    <action type="shell_command">make</action>
                    <action type="move_file">
                        <source>hisat</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>hisat-align</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>hisat-build</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>hisat-inspect</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>extract_splice_sites.py</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                </actions>
            </actions_group>
            <actions>
                <action type="chmod">
                    <file mode="750">$INSTALL_DIR/bin/hisat</file>
                </action>
                <action type="chmod">
                    <file mode="750">$INSTALL_DIR/bin/hisat-align</file>
                </action>
                <action type="chmod">
                    <file mode="750">$INSTALL_DIR/bin/hisat-build</file>
                </action>
                <action type="chmod">
                    <file mode="750">$INSTALL_DIR/bin/hisat-inspect</file>
                </action>
                <action type="chmod">
                    <file mode="750">$INSTALL_DIR/bin/extract_splice_sites.py</file>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme />
    </package>
</tool_dependency>