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Fixes courtesy of Peter Briggs: metagenomics.py: - Groups class: Fix for when second column not present - Axes class: make 'sniff' method more sensitive to try and restrict arbitrary tabular data uploads being sniffed as this type mothur_wrapper.py: - update cmd_dict['chimera.perseus'], to use correct inputs - add --beta option (needed for chimera.perseus tool) - add function for converting input floats from scientific notation (e.g. 1e-6, which mothur can't handle) to decimal format (e.g. 0.00001, which it can) chimera.perseus.xml: - add output data item for the "accnos" file (not previous captured in the history) trim.flows.xml: - cosmetic change: base name for additional output data items is now "trim.flows", rather than "logfile" (clarifies history items) shhh.flows.xml: - cosmetic change: update default value specified in help for mindiff to be consistent with that given in the mothur documentation
author Jim Johnson <jj@umn.edu>
date Wed, 04 Sep 2013 10:51:34 -0500
parents 49058b1f8d3f
children 1be61ceb20d7
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<?xml version="1.0"?>
<tool_dependency>
    <package name="mothur" version="1.27">
        <install version="1.0">
            <actions>
                <action type="download_by_url">http://www.mothur.org/w/images/c/cb/Mothur.1.27.0.zip</action>
                <action type="shell_command">chmod u+x Mothur.source/uchime_src/mk</action>
                <action type="shell_command">cd Mothur.source &amp;&amp; make</action>
                <action type="move_file">
                    <source>Mothur.source/mothur</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="move_file">
                    <source>Mothur.source/uchime</source>
                    <destination>$INSTALL_DIR/bin</destination>
                </action>
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
                    <environment_variable name="MOTHUR_MAX_PROCESSORS" action="set_to">2</environment_variable>
                </action>
            </actions>
        </install>
        <readme>
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

        </readme>
    </package>
    <!-- 
      http://supfam.cs.bris.ac.uk/TreeVector/treevectorsource.zip
    -->
</tool_dependency>