Mercurial > repos > iuc > package_stacks_1_40

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_stacks_1_40 commit e1c1550e0bd61c88ffead2b1c4f6ab7393052393
author iuc
date Sat, 25 Jun 2016 17:24:08 -0400
parents 95cffefc0dfe
children
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<?xml version="1.0"?>
<tool_dependency>
    <package name="samtools" version="0.1.19">
        <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="stacks" version="1.40">
        <install version="1.0">
            <actions>
                <action sha256sum="bf2304ba4ec44991db327ea77eb0f8c58de6d665162abf72470f5cd9dfb71493" type="download_by_url">https://depot.galaxyproject.org/software/stacks/stacks_1.40_src_all.tar.gz</action>

                <action type="set_environment_for_install">
                    <repository changeset_revision="c9bd782f5342" name="package_samtools_0_1_19" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="samtools" version="0.1.19" />
                    </repository>
                </action>

                <action type="shell_command">./configure --prefix=$INSTALL_DIR --enable-bam --with-bam-include-path=${BAM_INCLUDE} --with-bam-lib-path=${BAM_LIB_PATH}</action>
                <action type="shell_command">make</action>
                <action type="shell_command">make install</action>
                <!-- create env.sh -->
                <action type="set_environment">
                        <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin/</environment_variable>
                        <environment_variable action="set_to" name="STACKS_ROOT_DIR">$INSTALL_DIR/</environment_variable>
                </action>
           </actions>
        </install>
        <readme>
            This package installs STACKS from the sources available. Based on Cyril Monjeuad version
        </readme>
    </package>
</tool_dependency>