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Patch minimus2 during install (bug reported in 2011 not yet fixed in amos source)
author Jim Johnson <jj@umn.edu>
date Fri, 19 Jul 2013 08:01:23 -0500
parents 8ed847ebac73
children
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line source

<?xml version='1.0' encoding='utf-8'?>
<tool_dependency>
    <package name="boost" version="1.53.0">
        <repository changeset_revision="a72f8efe9201" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
    </package>
    <package name="mummer" version="3.23">
        <repository changeset_revision="8268327cce24" name="package_mummer_3_23" owner="jjohnson" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu/" />
    </package>
    <package name="amos" version="3.1.0">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://sourceforge.net/projects/amos/files/amos/3.1.0/amos-3.1.0.tar.gz</action>
                <!-- patch this, since it has been a bug since 2011 -->
                <action type="shell_command">sed -i.bak 's/dumpreads \(\$[(]BANK[)]\) \(-[mM]\) \(\$[(]REFCOUNT[)]\)/dumpreads \2 \3 \1/' src/Pipeline/minimus2.acf</action>
                <action type="shell_command">./configure --prefix=$INSTALL_DIR</action>
                <action type="shell_command">make</action>
                <action type="shell_command">make install</action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
http://sourceforge.net/projects/amos/
AMOS is a collection of tools and class interfaces for the assembly of DNA reads. The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation.
        </readme>
    </package>
</tool_dependency>