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<?xml version="1.0"?>
<tool_dependency>
    <package name="trinityrnaseq" version="2013_08_14">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://tools.osdd.jnu.ac.in/ngsap/trinityrnaseq_r20140717.tar.gz</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>
                <action type="set_environment">
                    <environment_variable name="TRINITY_HOME" action="set_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
        </readme>
    </package>
 <package name="samtools" version="0.1.18">
        <install version="1.0">
            <actions_group>
                <actions os="linux" architecture="i386">
                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.18-linux-i386.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions os="linux" architecture="x86_64">
                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions os="darwin" architecture="i386">
                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.18-Darwin-i386.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions os="darwin" architecture="x86_64">
                    <action type="download_by_url" target_filename="samtools-0.1.18.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.18-Darwin-x86_64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions>
                    <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.18.tar.bz2</action>
                    <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
                    <action type="shell_command">make</action>
                    <action type="move_file">
                        <source>samtools</source>
                        <destination>$INSTALL_DIR/bin</destination>
                    </action>
                    <action type="move_file">
                        <source>libbam.a</source>
                        <destination>$INSTALL_DIR/lib</destination>
                    </action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR/include/bam</destination_directory>
                    </action>
                </actions>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
                    <environment_variable name="BAM_ROOT" action="set_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme>
        </readme>
    </package>
<package name="rsem" version="1.1.17">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://deweylab.biostat.wisc.edu/rsem/src/rsem-1.1.17.tar.gz</action>
                <action type="shell_command">make</action>
                <action type="make_directory">$INSTALL_DIR/bin/sam</action> 
                <action type="move_file">
                    <source>sam/samtools</source>
                    <destination>$INSTALL_DIR/bin/sam</destination>
                </action>
                <action type="move_file">
                    <source>convert-sam-for-rsem</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>extract-transcript-to-gene-map-from-trinity</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-bam2readdepth</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-bam2wig</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-build-read-index</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-calculate-credibility-intervals</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-calculate-expression</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-extract-reference-transcripts</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-gen-transcript-plots</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-get-unique</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-parse-alignments</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-plot-model</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-plot-transcript-wiggles</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-prepare-reference</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-preref</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-run-em</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-run-gibbs</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-simulate-reads</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-synthesis-reference-transcripts</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>rsem-tbam2gbam</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
        </readme>
    </package>
  <package name="eXpress" version="1.5.1">
        <install version="1.0">
            <actions_group>
                <actions os="linux" architecture="x86_64">
                    <action type="download_by_url">http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-linux_x86_64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>
                </actions>
                <actions os="darwin" architecture="x86_64">
                    <action type="download_by_url">http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-macosx_x86_64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR/bin</destination_directory>
                    </action>
                </actions>
                <actions>
                    <action type="download_by_url">http://bio.math.berkeley.edu/eXpress/downloads/express-1.5.1/express-1.5.1-src.tgz</action>
                    <action type="shell_command">cmake src -DCMAKE_INSTALL_PREFIX:PATH=$INSTALL_DIR</action>
                    <action type="shell_command">make &amp;&amp; make install</action>
                </actions>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme></readme>
    </package>
 <package name="bowtie" version="0.12.7">
        <install version="1.0">
            <actions_group>
                <actions os="linux" architecture="x86_64">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/bowtie/bowtie-0.12.7-linux-x86_64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions os="darwin" architecture="x86_64">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/bowtie/bowtie-0.12.7-macos-10.5-x86_64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions os="linux" architecture="i386">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/bowtie/bowtie-0.12.7-linux-i386.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions os="darwin" architecture="i386">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/i386/bowtie/bowtie-0.12.7-macos-10.5-i386.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions>
                    <action type="download_by_url">http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.7/bowtie-0.12.7-src.zip</action>
                    <action type="shell_command">make</action>
                    <action type="move_file">
                        <source>bowtie</source>
                        <destination>$INSTALL_DIR</destination>
                    </action>
                    <action type="move_file">
                        <source>bowtie-build</source>
                        <destination>$INSTALL_DIR</destination>
                    </action>
                    <action type="move_file">
                        <source>bowtie-inspect</source>
                        <destination>$INSTALL_DIR</destination>
                    </action>
                </actions>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme></readme>
    </package>
  <package name="bowtie2" version="2.1.0">
        <install version="1.0">
            <actions_group>
                <actions os="linux" architecture="x86_64">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/x86_64/bowtie2/bowtie2-2.1.0-linux-x86_64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions os="darwin" architecture="x86_64">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/x86_64/bowtie2/bowtie2-2.1.0-macos-x86_64.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions os="linux" architecture="i386">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/linux/i386/bowtie2/bowtie2-2.1.0-linux-i386.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <actions os="darwin" architecture="i386">
                    <action type="download_by_url">http://depot.galaxyproject.org/package/darwin/i386/bowtie2/bowtie2-2.1.0-macos-i386.tgz</action>
                    <action type="move_directory_files">
                        <source_directory>.</source_directory>
                        <destination_directory>$INSTALL_DIR</destination_directory>
                    </action>
                </actions>
                <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>$INSTALL_DIR</destination>
                    </action>
                    <action type="move_file">
                        <source>bowtie2-align</source>
                        <destination>$INSTALL_DIR</destination>
                    </action>
                    <action type="move_file">
                        <source>bowtie2-build</source>
                        <destination>$INSTALL_DIR</destination>
                    </action>
                    <action type="move_file">
                        <source>bowtie2-inspect</source>
                        <destination>$INSTALL_DIR</destination>
                    </action>
                </actions>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
                </action>
            </actions_group>
        </install>
        <readme></readme>
    </package>
<package name="tophat2" version="2.0.9">
        <repository toolshed="http://toolshed.g2.bx.psu.edu" name="tophat2" owner="devteam" changeset_revision="ae06af1118dc" />
</package>
</tool_dependency>