| Next changeset 1:de3ada25282e (2012-05-31) |
|
Commit message:
Uploaded |
|
added:
pb.pl pb.xml phylobayes_README.txt |
| b |
| diff -r 000000000000 -r bbf0d9e9b82a pb.pl --- /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; |
| b |
| diff -r 000000000000 -r bbf0d9e9b82a pb.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/pb.xml Thu May 31 19:44:16 2012 -0400 |
| b |
| @@ -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> |
| b |
| diff -r 000000000000 -r bbf0d9e9b82a phylobayes_README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/phylobayes_README.txt Thu May 31 19:44:16 2012 -0400 |
| b |
| @@ -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 \ No newline at end of file |