Mercurial > repos > jjohnson > mothur_toolsuite

view mothur/tool_dependencies.xml @ 34:1be61ceb20d7

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Updated tool_dependencies.xml to build mothur package on Linux (may break other OSes).
author pjbriggs
date Mon, 22 Sep 2014 11:19:09 -0400
parents 49058b1f8d3f
children 95d75b35e4d2
line wrap: on
line source

<?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>
		<!-- Update the makefile -->
		<action type="shell_command">sed -i 's/^USECOMPRESSION ?= no/USECOMPRESSION ?= yes/' Mothur.source/makefile</action>
		<action type="shell_command">sed -i 's/TARGET_ARCH += -arch x86_64/#TARGET_ARCH += -arch x86_64/' Mothur.source/makefile</action>
		<action type="shell_command">sed -i 's/#CXXFLAGS +=/CXXFLAGS +=/' Mothur.source/makefile</action>
		<!-- Update the uchime_src/mk -->
		<action type="shell_command">sed -i 's/LINK_OPTS=-static/LINK_OPTS=/' Mothur.source/uchime_src/mk</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>