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changeset 0:bbf0d9e9b82a draft

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author ucsb-phylogenetics
date Thu, 31 May 2012 19:44:16 -0400
parents
children de3ada25282e
files pb.pl pb.xml phylobayes_README.txt
diffstat 3 files changed, 148 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pb.pl	Thu May 31 19:44:16 2012 -0400
@@ -0,0 +1,26 @@
+#!/usr/bin/perl
+
+# Perl wrapper script written by: Roger Ngo and Todd H. Oakley, UCSB
+
+
+my $phylobayes_path = '/home/galaxy/pkgs/phylobayes3.3b/exe_lin64/pb';
+my $readPB_path = '/home/galaxy/pkgs/phylobayes3.3b/exe_lin64/readpb';
+
+my $fileName = $ARGV[0];
+my $nchainInput = $ARGV[1];
+my $cycle_bp_trace_comp = $ARGV[2];
+my $discrepancies_threshold = $ARGV[3];
+my $effective_size_floor = $ARGV[4];
+my $jobName = "dataset";
+
+my $burnin = $ARGV[5];
+my $sampleInterval = $ARGV[6];
+
+my $run1 = qx/$phylobayes_path -d $fileName -nchain $nchainInput $cycle_bp_trace_comp $discrepancies_threshold $effective_size_floor $jobName 2>errorlog/;
+print $run1;
+
+my $list = qx/ls -l/;
+print $list;
+
+my $run2 = qx/$readPB_path -x $burnin $sampleInterval $jobName 2>errorlog/;
+print $run2;
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/pb.xml	Thu May 31 19:44:16 2012 -0400
@@ -0,0 +1,52 @@
+<tool id="phylobayes" name="Phylobayes">
+	<description>Runs phylobayes</description>
+	<command interpreter="perl">pb.pl $filename $nchain $cycles $discrepancies $effectivesize $burnin $sampleInterval</command>
+	<inputs>
+		<param name="filename" type="data" format="txt" label="Input file (ali)" />
+		<param name="nchain" type="integer" value="0" label="Number of chains to run" />
+		<param name="cycles" type="integer" value="0" label="Cycle interval to run bpcomp and tracecomp" />
+		<param name="discrepancies" type="float" value="0.0" label="Discrepancies ceiling" />
+		<param name="effectivesize" type="integer" value="0" label="Effective sizes floor"/>
+		<param name="burnin" type="integer" value="0" label="Post analysis burnin" />
+		<param name="sampleInterval" type="integer" value="0" label="Post analysis sample interval"/>
+	</inputs>
+	<outputs>
+		<data from_work_dir="dataset.con.tre" name="contre" format="txt" />
+		<data from_work_dir="dataset.bplist" name="bplist" format="txt" />
+	</outputs>
+	
+	<help>
+	Phylobayes - Bayesian phylogenetic software based on mixture models.
+	Lartillot N., Philippe H. Molecular Biology and Evolution. 2004 21(6):1095-1109. 
+	
+	PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. 
+	Compared to other phylogenetic MCMC samplers (e.g. MrBayes ), the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT. 
+	It is particularly well suited for large multigene alignments, such as those used in phylogenomics. 
+
+	The version 2.3 of phylobayes allows for divergence time estimation, posterior predictive analyses, including compositional homogeneity and saturation tests, 
+	data recoding (analogous to R/Y coding, but for amino-acids), and cross-validation. It also implements a more efficient tree searching MCMC algorithm. 
+
+	http://www.atgc-montpellier.fr/phylobayes/
+	
+	"A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process."
+	http://www.atgc-montpellier.fr/download/papers/cat_2004.pdf
+	Lartillot N., Philippe H.
+	Molecular Biology and Evolution. 2004 21(6):1095-1109.
+	
+	"Computing Bayes factors using thermodynamic integration."
+	http://www.atgc-montpellier.fr/download/papers/phylobayes_2006.pdf
+	Lartillot N., Philippe H.
+	Systematic Biology. 2006 55:195-207.
+	
+	Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model."
+	http://www.atgc-montpellier.fr/download/papers/cat_2007.pdf
+	Lartillot N., Brinkmann H., Philippe H.
+	BMC Evolutionary Biology. 2007 Feb 8;7 Suppl 1:S4.
+	
+	"Phylogenomics."
+	http://www.atgc-montpellier.fr/download/papers/phylogenomics_2005.pdf
+	Philippe H., Delsuc F., Brinkmann H., Lartillot N.
+	Annual Review of Ecology, Evolution and Systematics. 2005 36,541-562.
+
+	</help>
+</tool>
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/phylobayes_README.txt	Thu May 31 19:44:16 2012 -0400
@@ -0,0 +1,70 @@
+Phylobayes Galaxy Installation and Configuration Instructions
+
+Phylobayes original binaries written by: Lartillot N., Philippe H. Molecular Biology and Evolution
+
+Galaxy and Perl wrapper script written by: Roger Ngo and Todd H. Oakley, UCSB
+
+
+	Phylobayes - Bayesian phylogenetic software based on mixture models.
+	Lartillot N., Philippe H. Molecular Biology and Evolution. 2004 21(6):1095-1109. 
+	
+	PhyloBayes is a Bayesian Monte Carlo Markov Chain (MCMC) sampler for phylogenetic reconstruction using protein alignments. 
+	Compared to other phylogenetic MCMC samplers (e.g. MrBayes ), the main distinguishing feature of PhyloBayes is the underlying probabilistic model, CAT. 
+	It is particularly well suited for large multigene alignments, such as those used in phylogenomics. 
+
+	The version 2.3 of phylobayes allows for divergence time estimation, posterior predictive analyses, including compositional homogeneity and saturation tests, 
+	data recoding (analogous to R/Y coding, but for amino-acids), and cross-validation. It also implements a more efficient tree searching MCMC algorithm. 
+
+	http://www.atgc-montpellier.fr/phylobayes/
+	
+	"A Bayesian Mixture Model for Across-Site Heterogeneities in the Amino-Acid Replacement Process."
+	http://www.atgc-montpellier.fr/download/papers/cat_2004.pdf
+	Lartillot N., Philippe H.
+	Molecular Biology and Evolution. 2004 21(6):1095-1109.
+	
+	"Computing Bayes factors using thermodynamic integration."
+	http://www.atgc-montpellier.fr/download/papers/phylobayes_2006.pdf
+	Lartillot N., Philippe H.
+	Systematic Biology. 2006 55:195-207.
+	
+	Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model."
+	http://www.atgc-montpellier.fr/download/papers/cat_2007.pdf
+	Lartillot N., Brinkmann H., Philippe H.
+	BMC Evolutionary Biology. 2007 Feb 8;7 Suppl 1:S4.
+	
+	"Phylogenomics."
+	http://www.atgc-montpellier.fr/download/papers/phylogenomics_2005.pdf
+	Philippe H., Delsuc F., Brinkmann H., Lartillot N.
+	Annual Review of Ecology, Evolution and Systematics. 2005 36,541-562.
+
+
+
+Included in this package:
+
+* pb.pl - Perl wrapper script for the Galaxy tool
+* pb.xml - Galaxy Phylobayes XML file
+* phylobayes_README - Documentation file
+
+Dependencies: PHYLOBAYES 3.3b must be installed on the Galaxy user account.
+
+How to install Phylobayes
+
+1. Ensure phylobayes 3.3b is installed.
+
+2. Modify the $phylobayes_path and $readPB_path to reflect the location
+of pb and readpb in your user account. The default is listed below:
+
+my $phylobayes_path = '/home/galaxy/pkgs/phylobayes3.3b/exe_lin64/pb';
+my $readPB_path = '/home/galaxy/pkgs/phylobayes3.3b/exe_lin64/readpb';
+
+3. Copy pb.pl and pb.xml to a folder in the /galaxy-dist/tools directory.
+
+4. Add the XML tool into the tool_conf.xml file in galaxy-dist/
+
+5. Restart Galaxy with:
+
+./run.sh --stop-daemon
+
+and then
+
+./run.sh --reload --daemon
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