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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/packages/package_mothur_1_36_1 commit e23a8ad798830209db722d5496d19ec7a5e06214
author iuc
date Mon, 01 Aug 2016 14:34:05 -0400
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<?xml version="1.0"?>
<tool_dependency>
    <package name="mothur" version="1.36.1">
        <install version="1.0">
            <actions>
                <action sha256sum="dfdc486b24d14d776d45df9d523e62a49332ff0e3def4e0bb95cfbe369638f22" type="download_by_url">https://github.com/mothur/mothur/archive/v1.36.1.zip</action>
                <action type="set_environment_for_install">
                    <repository changeset_revision="67fbfb9fcec2" name="package_legacy_blast_2_2_22" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="legacy_blast" version="2.2.22" />
                    </repository>
                    <repository changeset_revision="a0dd39685fce" name="package_boost_1_57" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="boost" version="1.57" />
                    </repository>
                    <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
                        <package name="zlib" version="1.2.8" />
                    </repository>
                </action>
                <action type="shell_command">chmod u+x source/uchime_src/mk</action>
                <action type="shell_command">
                    test $(uname) = Linux &amp;&amp;
                    perl -i.bak -pe 's/(USEREADLINE.+) = yes/$1 = no/; s/TARGET_ARCH \+= -arch x86_64//; s/#(CXXFLAGS.+-mtune=native -march=native -m64)/$1/;' source/makefile ||
                    true
                </action>
                <action type="shell_command">sed -i.bak -e 's/\ \ \ \ /\t/g' source/makefile;</action>
                <action type="shell_command">sed -i.bak -e '141d;151d;152d' source/makefile;</action>
                <action type="shell_command">sed -i.bak -e 's/fortranSource//g' source/makefile;</action>
                <action type="shell_command">sed -i.bak -e 's/\/usr\/local/${BOOST_ROOT_DIR}\/boost/g' source/makefile;</action>
                <action type="shell_command">sed -i.bak -e 's/\${BOOST_LIBRARY_DIR}zlib.a/${ZLIB_ROOT_DIR}\/lib\/libz.a/' source/makefile</action>

                <action type="shell_command">cd source; make -j 2;</action>
                <action type="move_file">
                    <source>mothur</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>source/uchime</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
                </action>
                <action type="make_directory">$INSTALL_DIR/bin/blast/bin</action>
                <action type="change_directory">$INSTALL_DIR/bin</action>
                <action type="shell_command">cd $INSTALL_DIR/bin;mypath=`which blastall`; mypath=`dirname $mypath`; cp $mypath/* ./blast/bin</action>
            </actions>
        </install>
        <readme>
*Authors &amp; Contacts*
Jim Johnson
Peter Briggs
Iyad Kandalaft | Iyad.Kandalaft@Agr.gc.ca | Agriculture and Agri-Foods Canada
Kevin Chen | Agriculture and Agri-Foods Canada

*Description*

The Mothur Tool Suite repository provides Galaxy wrappers for the majority of the Mothur tools.  In addition, it downloads and builds the Mothur binaries.

Supports Linux environments such as Redhat/Centos/Ubuntu as well as Mac OSX.

These links provide information for building the Mothur package in most environments.

http://www.mothur.org/wiki/Download_mothur

http://www.mothur.org/wiki/Installation
http://www.mothur.org/wiki/Makefile_options

*Requirements*

- build tools (make, C libraries, GCC)
- libncurses-dev(el)
- simplejson (python library)
        </readme>
    </package>
    <package name="legacy_blast" version="2.2.22">
        <repository changeset_revision="67fbfb9fcec2" name="package_legacy_blast_2_2_22" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
    </package>
    <package name="boost" version="1.57">
        <repository changeset_revision="a0dd39685fce" name="package_boost_1_57" 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>
</tool_dependency>