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changeset 1:de3ada25282e draft

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author ucsb-phylogenetics
date Thu, 31 May 2012 19:50:40 -0400
parents bbf0d9e9b82a
children 4de3f9572615
files pb.pl pb.xml phylobayes_README.txt
diffstat 3 files changed, 0 insertions(+), 148 deletions(-) [+]
line wrap: on
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--- a/pb.pl	Thu May 31 19:44:16 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,26 +0,0 @@
-#!/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;
--- a/pb.xml	Thu May 31 19:44:16 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,52 +0,0 @@
-<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>
--- a/phylobayes_README.txt	Thu May 31 19:44:16 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-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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