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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_trinity_2_0_6 commit 993ba7c18dcabb15aa76bca2fcc9211a5f58bf1d
author iuc
date Fri, 20 Nov 2015 06:49:06 -0500
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<?xml version="1.0"?>
<tool_dependency>
    <package name="ncurses" version="5.9">
        <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" 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="trinity" version="2.0.6">
        <install version="1.0">
            <actions>
                <action sha256sum="e0c3ec885fdcfe3422ea492372518ddf5d1aed3daa187c69c4254516b0845de1" type="download_by_url">https://github.com/trinityrnaseq/trinityrnaseq/archive/v2.0.6.tar.gz</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="5e1760c773ba" name="package_ncurses_5_9" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="ncurses" version="5.9" />
                    </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/' trinity-plugins/Makefile</action>
                <action type="shell_command">sed -i.bak -e 's/-ltinfo//' trinity-plugins/Makefile</action> <!-- tinfo is included in ncurses lib-->
                <action type="shell_command">sed -i.bak -e '/tar -zxvf ${RSEM_CODE}.tar.gz/a \\tsed -i.bak -e "s|-lz|-lz -L${ZLIB_ROOT_PATH}/lib|" ${RSEM_CODE}/Makefile ${RSEM_CODE}/sam/Makefile' trinity-plugins/Makefile</action> <!-- In case you have an obsolete zlib in /usr/lib -->
                <action type="shell_command">make</action>
                <action type="shell_command">make plugins</action>

                <action type="move_file">
                    <source>Trinity</source>
                    <destination>$INSTALL_DIR</destination>
                </action>
                <action type="move_directory_files">
                    <source_directory>Analysis</source_directory>
                    <destination_directory>$INSTALL_DIR/Analysis</destination_directory>
                </action>
                <action type="move_directory_files">
                    <source_directory>Butterfly</source_directory>
                    <destination_directory>$INSTALL_DIR/Butterfly</destination_directory>
                </action>
                <action type="move_directory_files">
                    <source_directory>Chrysalis</source_directory>
                    <destination_directory>$INSTALL_DIR/Chrysalis</destination_directory>
                </action>
                <action type="move_directory_files">
                    <source_directory>Inchworm</source_directory>
                    <destination_directory>$INSTALL_DIR/Inchworm</destination_directory>
                </action>
                <action type="move_directory_files">
                    <source_directory>PerlLib</source_directory>
                    <destination_directory>$INSTALL_DIR/PerlLib</destination_directory>
                </action>
                <action type="move_directory_files">
                    <source_directory>trinity-plugins</source_directory>
                    <destination_directory>$INSTALL_DIR/trinity-plugins</destination_directory>
                </action>
                <action type="move_directory_files">
                    <source_directory>util</source_directory>
                    <destination_directory>$INSTALL_DIR/util</destination_directory>
                </action>

                <action type="shell_command">rm $INSTALL_DIR/trinity-plugins/*tar.gz</action>

                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/util</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/collectl/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/fastool</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/jellyfish/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/parafly/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/transdecoder</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/Trimmomatic</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/slclust/bin</environment_variable>
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/trinity-plugins/GAL_0.2.1</environment_variable>
                </action>
            </actions>
        </install>
    </package>
</tool_dependency>