annotate mothur/tool_dependencies.xml @ 35:95d75b35e4d2

Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)

<?eml 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">
									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>
							</actions>
						</install>
						<readme>

							Iyad Kandalaft added shell commands to build in Linux environment such as Redhat/Centos/Ubuntu. ReadLine libraries are not required.  libncurses-devel are required.

							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>
-->
					<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 -e /etc/redhat-release &amp;&amp;
			perl -i.bak -pe 's/#(CXX.+g\+\+44)/$1/;' Mothur.source/makefile ||
			true
		</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="32c158152e5e" name="package_blast_plus_2_2_26" owner="meowmeow" toolshed="http://onotta669816x:9001/">
										<package name="blast" version="2.2.26" />
								</repository>
							</action>

									<!--	
								<action type="shell_command">mkdir $INSTALL_DIR/bin/blast; mkdir $INSTALL_DIR/bin/blast/bin;</action>
								-->
								<action type="make_directory">$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; cp ../../../../../../blast/*/*/package_blast_plus_2_2_26/*/* ./blast/bin</action>
								-->

								<action type="shell_command">cd $INSTALL_DIR/bin;mypath=`which blastall`; mypath=`dirname $mypath`; cp $mypath/* ./blast/bin</action>

							</actions>
						</install>
						<readme>

							Iyad Kandalaft added shell commands to build in Linux environment such as Redhat/Centos/Ubuntu. ReadLine libraries are not required.  libncurses-devel are required.

							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
	-->

			<package name="blast" version="2.2.26">
				<repository 
					name="package_blast_plus_2_2_26"
					owner="meowmeow" 
					changeset_revision="32c158152e5e"
					toolshed="http://onotta669816x:9001/"
					prior_installation_required="True"/>
			</package>

		</tool_dependency>