Mercurial > repos > jjohnson > mothur_toolsuite

diff mothur/tool_dependencies.xml @ 35:95d75b35e4d2

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Updated tools to use Mothur 1.33. Added some misc. fixes and updates (blast repository, tool fixes)
author certain cat
date Fri, 31 Oct 2014 15:09:32 -0400
parents 1be61ceb20d7
children 040410b8167e
line wrap: on
line diff
--- a/mothur/tool_dependencies.xml	Mon Sep 22 11:19:09 2014 -0400
+++ b/mothur/tool_dependencies.xml	Fri Oct 31 15:09:32 2014 -0400
@@ -1,44 +1,122 @@
-<?xml version="1.0"?>
+<?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>
-		<!-- 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 .
+	<!--
+	<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
 
-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>
 
-        </readme>
-    </package>
-    <!-- 
-      http://supfam.cs.bris.ac.uk/TreeVector/treevectorsource.zip
-    -->
-</tool_dependency>
+									<!--	
+								<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>
+