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Commit message:
Deleted selected files |
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removed:
pb.pl pb.xml phylobayes_README.txt |
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| diff -r bbf0d9e9b82a -r de3ada25282e pb.pl --- a/pb.pl Thu May 31 19:44:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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; |
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| diff -r bbf0d9e9b82a -r de3ada25282e pb.xml --- a/pb.xml Thu May 31 19:44:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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> |
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| diff -r bbf0d9e9b82a -r de3ada25282e phylobayes_README.txt --- a/phylobayes_README.txt Thu May 31 19:44:16 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -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 \ No newline at end of file |