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diff mothur/tool_dependencies.xml @ 36:040410b8167e default tip

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Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.
author galaxyuser <galaxy_user@agr.g.ca>
date Mon, 10 Nov 2014 15:40:02 -0500
parents 95d75b35e4d2
children
line wrap: on
line diff
--- a/mothur/tool_dependencies.xml	Fri Oct 31 15:09:32 2014 -0400
+++ b/mothur/tool_dependencies.xml	Mon Nov 10 15:40:02 2014 -0500
@@ -1,122 +1,77 @@
-<?eml version="1.0"?>
+<?xml version="1.0"?>
 <tool_dependency>
-	<!--
-	<package name="mothur" version="1.27">
+	<package name="mothur" version="1.33">
 		<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="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>
-							</actions>
-						</install>
-						<readme>
+				<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>
 
-							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 .
+				<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>
 
-							http://www.mothur.org/wiki/Download_mothur
-
-							http://www.mothur.org/wiki/Installation
-
-							http://www.mothur.org/wiki/Makefile_options
+				<action type="shell_command">cd $INSTALL_DIR/bin;mypath=`which blastall`; mypath=`dirname $mypath`; cp $mypath/* ./blast/bin</action>
 
-						</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>
+			</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
 
-									<!--	
-								<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>
-								-->
+http://www.mothur.org/wiki/Installation
+http://www.mothur.org/wiki/Makefile_options
 
-								<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 .
+*Requirements*
 
-							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>
+- 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>