<?xml version="1.0"?>
<tool_dependency>
	<package name="mothur" version="1.33">
		<install version="1.0">
			<actions>
				<action type="download_by_url">http://www.mothur.org/w/images/6/65/Mothur.1.33.3.zip</action>
				<action type="shell_command">chmod u+x Mothur.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)/$1/;' Mothur.source/makefile ||
					true
				</action>
				<action type="shell_command">cd Mothur.source; make -j 2;</action>
				<action type="move_file">
					<source>Mothur.source/mothur</source>
					<destination>$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>
				<action type="set_environment_for_install">
					<repository changeset_revision="8a5a4d8db315" name="package_blast_2_2_26" owner="iyad" toolshed="https://toolshed.g2.bx.psu.edu/">
						<package name="blast" version="2.2.26" />
					</repository>
				</action>

				<action type="make_directory">$INSTALL_DIR/bin/blast</action>
				<action type="make_directory">$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="blast" version="2.2.26">
		<repository 
			name="package_blast_2_2_26"
			owner="iyad"
			changeset_revision="8a5a4d8db315"
			toolshed="https://toolshed.g2.bx.psu.edu/"
			prior_installation_required="True"/>
	</package>

		</tool_dependency>