# HG changeset patch
# User galaxyuser <galaxy_user@agr.g.ca>
# Date 1415652002 18000
# Node ID 040410b8167e3c57ee8ae1a6ef33bfcdf14ad7c2
# Parent  95d75b35e4d21474195a9489ff527576ee2cee1e
Fixed reference to legacy blast repository in tool_dependencies.xml. Updated README with author information.

diff -r 95d75b35e4d2 -r 040410b8167e mothur/README
--- a/mothur/README	Fri Oct 31 15:09:32 2014 -0400
+++ b/mothur/README	Mon Nov 10 15:40:02 2014 -0500
@@ -1,20 +1,15 @@
-Provides galaxy tools for the Mothur metagenomics package -  http://www.mothur.org/wiki/Main_Page 
-
+Galaxy wrappers for the Mothur metagenomics tools (http://www.mothur.org/wiki/Main_Page)
 
-Mothur should be able to be auto-installed as a tool_dependency
-  You may want to reorganize the tool panel after installing
-  See below: Reorganize integrated_tool_panel.xml
-  This was based on: http://www.mothur.org/wiki/Mothur_manual
-  (The environment variable MOTHUR_MAX_PROCESSORS can be used to limit the number of cpu processors used for mothur commands)
-   This will be set in: tool_dependencies/mothur/1.27/jjohnson/mothur_toolsuite/*/env.sh
-	Requirements for auto installation:
-	-	make (sudo-apt get install make)
-	- g++ (sudo apt-get install g++)
-	- gfortran (sudo apt-get install gfortran)
-	- pip (sudo apt-get install python-pip)
+The Mothur Tool Suite repository:
+	- Provides Mothur wrappers for most Mothur tools
+	- Data type used by mothur and other metagenomics tools
+	- Downloads and builds Mothur on the Linux or Mac operating system
+
+Requirements:
+	- Build utilities (make, GCC, gfortran, etc)
 	- simplejson (pip install simplejson)
 
-	Repository Dependency: 
+Repository Dependency: 
 	- BLAST Legacy ver. 2.2.26 (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/LATEST/)
 	- The repository name should be package_blast_2_2_26 so it matches with the tool dependency.
 	
@@ -114,29 +109,23 @@
     /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.fasta
     /project/db/galaxy/mothur/RDP/trainset7_112011.rdp.tax
 
-
-
 Add tool-data:  (contains  pointers to silva, greengenes, and RDP reference data)
   tool-data/mothur_aligndb.loc
   tool-data/mothur_map.loc
   tool-data/mothur_taxonomy.loc
   tool-data/shared/jars/TreeVector.jar
 
-
 ################################################################
 #### If you are manually adding this to your local galaxy:  ####
 ################################################################
 
 add config files (*.xml) and wrapper code (*.py) from tools/mothur/*  to your galaxy installation 
 
-
 add datatype definition file: lib/galaxy/datatypes/metagenomics.py
 
 add the following import line to:  lib/galaxy/datatypes/registry.py
 import metagenomics # added for metagenomics mothur
 
-
-
 add datatypes to:  datatypes_conf.xml
 
 add mothur tools to:   tool_conf.xml
@@ -172,7 +161,3 @@
  # Each item  conatins:   a regex pattern for matching filenames and  a galaxy datatype (separated by :)
  # The regex match.groups()[0] is used as the id name of the dataset, and must result in  unique name for each output
  --new_datasets='^\S+?\.((\S+)\.(unique|[0-9.]*)\.dist)$:lower.dist'
-
- ## 
- ## NOTE:   The "read" commands were eliminated with Mothur version 1.18
- ##
diff -r 95d75b35e4d2 -r 040410b8167e mothur/tool_data_table_conf.xml.sample
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/mothur/tool_data_table_conf.xml.sample	Mon Nov 10 15:40:02 2014 -0500
@@ -0,0 +1,18 @@
+<tables>
+  <table name="mothur_aligndb" comment_char="#">
+    <columns>name, value</columns>
+    <file path="tool-data/mothur_aligndb.loc" />
+  </table>
+  <table name="mothur_lookup" comment_char="#">
+    <columns>name, value</columns>
+    <file path="tool-data/mothur_lookup.loc" />
+  </table>
+  <table name="mothur_map" comment_char="#">
+    <columns>name, value</columns>
+    <file path="tool-data/mothur_map.loc" />
+  </table>
+  <table name="mothur_taxonomy" comment_char="#">
+    <columns>name, value</columns>
+    <file path="tool-data/mothur_taxonomy.loc" />
+  </table>
+</tables>
\ No newline at end of file
diff -r 95d75b35e4d2 -r 040410b8167e mothur/tool_dependencies.xml
--- 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>
 
diff -r 95d75b35e4d2 -r 040410b8167e mothur/tools/mothur/pcr.seqs.xml
--- a/mothur/tools/mothur/pcr.seqs.xml	Fri Oct 31 15:09:32 2014 -0400
+++ b/mothur/tools/mothur/pcr.seqs.xml	Mon Nov 10 15:40:02 2014 -0500
@@ -40,7 +40,7 @@
   --result=#echo ','.join($results)
   --processors=8
   #if $pdiffs.__str__ != '' and int($pdiffs.__str__) > 0:
-   --pdiffs=$pdiffs
+   --$pdiffs=$pdiffs
   #end if
  </command>
  <inputs>