comparison tool_dependencies.xml @ 0:4567331d510a draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_rsem_1_2_28 commit 77385ec02b79f527348aff01bd83a019e30f5f45

0:4567331d510a

<?xml version="1.0"?>
<tool_dependency>
    <package name="ncurses" version="6.0">
        <repository changeset_revision="0efde9889efd" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="zlib" version="1.2.8">
        <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="rsem" version="1.2.28">
        <install version="1.0">
            <actions>
                <action sha256sum="b54c3ac0ab44b470ab0c29852d30b5194674e36375c3b9067eb3150f569de53e" type="download_by_url">
                    https://github.com/deweylab/RSEM/archive/v1.2.28.tar.gz
                </action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="0efde9889efd" name="package_ncurses_6_0" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="ncurses" version="6.0" />
                    </repository>
                    <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="zlib" version="1.2.8" />
                    </repository>
                </action>
                <action type="shell_command">sed -i.bak -e 's/-lcurses/-lncurses/' samtools*/Makefile samtools*/config.mk</action>
                <action type="shell_command">sed -i.bak -e "s|-lz|-lz -L${ZLIB_ROOT_PATH}/lib|" Makefile samtools*/Makefile</action> <!-- In case you have an obsolete zlib in /usr/lib -->
                <action type="shell_command">make</action>

                <action type="move_file">
                    <source>rsem-bam2readdepth</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-bam2wig</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-build-read-index</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-calculate-credibility-intervals</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-calculate-expression</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-control-fdr</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-extract-reference-transcripts</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-gen-transcript-plots</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-generate-data-matrix</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-generate-ngvector</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-get-unique</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-gff3-to-gtf</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-parse-alignments</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-plot-model</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-plot-transcript-wiggles</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-prepare-reference</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-preref</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-refseq-extract-primary-assembly</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-run-ebseq</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-run-em</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-run-gibbs</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-sam-validator</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-scan-for-paired-end-reads</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-simulate-reads</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-synthesis-reference-transcripts</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem-tbam2gbam</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_file">
                    <source>rsem_perl_utils.pm</source>
                    <destination>$INSTALL_DIR</destination>
                </action>

                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/</environment_variable>
                </action>
            </actions>
        </install>
    </package>
</tool_dependency>