Mercurial > repos > anmoljh > package_trinityrnaseq_r20140717

view tool_dependencies.xml @ 6:ae82c6c09b69

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few changes
author 'Anmol J. Hemrom' <anmol.jh@gmail.com>
date Thu, 03 Sep 2015 14:15:52 +0100
parents 03100f652146
children 484a0e253167
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<?xml version="1.0"?>
<tool_dependency>
    <package name="ncurses" version="5.9">
        <repository changeset_revision="93ce0192b9db" name="package_ncurses_5_9" owner="anmoljh" 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="trinityrnaseq" version="r20140717">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/trinityrnaseq/files/trinityrnaseq_r20140717.tar.gz</action>
		<action type="set_environment_for_install">
                    <repository changeset_revision="93ce0192b9db" name="package_ncurses_5_9"  owner="anmoljh" 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/rsem/sam/Makefile</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>
</tool_dependency>