Mercurial > repos > sanbi-uwc > mothur_test

diff tool_dependencies.xml.old @ 0:ee4fee239fe7 draft default tip

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planemo upload commit 68a4fd4cc5332c57ac39bef73db224425af0706c-dirty
author sanbi-uwc
date Fri, 03 Jun 2016 09:32:47 -0400
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml.old	Fri Jun 03 09:32:47 2016 -0400
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+<?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="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=""
+			changeset_revision=""
+			toolshed=""
+			prior_installation_required="True"/>
+	</package>
+
+		</tool_dependency>
+