| Previous changeset 2:4de3f9572615 (2012-06-21) Next changeset 4:5b23f3eb3f09 (2012-06-24) |
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Commit message:
Phylomatic and Phylobayes included |
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added:
ucsb_phylogenetics/phylobayes/pb.pl ucsb_phylogenetics/phylobayes/pb.xml ucsb_phylogenetics/phylobayes/phylobayes_README.txt ucsb_phylogenetics/phylobayes/phylobayes_wrapper.tar.bz2 ucsb_phylogenetics/phylomatic/phylomatic ucsb_phylogenetics/phylomatic/phylomatic.pl ucsb_phylogenetics/phylomatic/phylomatic.xml ucsb_phylogenetics/phylomatic/phylomatic_README.txt |
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removed:
phylomatic/phylomatic phylomatic/phylomatic.pl phylomatic/phylomatic.xml phylomatic/phylomatic_README.txt |
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| diff -r 4de3f9572615 -r 3db16e8335e1 phylomatic/phylomatic |
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| Binary file phylomatic/phylomatic has changed |
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| diff -r 4de3f9572615 -r 3db16e8335e1 phylomatic/phylomatic.pl --- a/phylomatic/phylomatic.pl Thu Jun 21 17:46:55 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,10 +0,0 @@ -#!/usr/bin/perl - -#wrapper written by Roger Ngo and Todd H Oakley, UCSB - -my $file1 = $ARGV[0]; -my $file2 = $ARGV[1]; - -my $run = qx/phylomatic -f $file1 -t $file2 > output.txt 2> errors.txt /; - -print $run; |
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| diff -r 4de3f9572615 -r 3db16e8335e1 phylomatic/phylomatic.xml --- a/phylomatic/phylomatic.xml Thu Jun 21 17:46:55 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,29 +0,0 @@ -<tool id="phylomatic" name="Phylomatic"> - <description>Run Phylomatic</description> - <command interpreter="perl">./phylomatic.pl $input1 $input2</command> - <inputs> - <param name="input1" type="data" format="txt" label="Phylogenetic Tree" /> - <param name="input2" type="data" format="txt" label="Taxonomy File" /> - </inputs> - - <outputs> - <data from_work_dir="output.txt"/> - </outputs> - - <help> - Phylomatic (Part of Phylocom) - - http://www.phylodiversity.net/phylomatic/phylomatic.html - - The online software takes your list of taxa, and first tries to match them by genus name to the megatree. - Failing that, they are attached by family name. If all the genera appear in the megatree, then that family appears resolved. - If even one genus is missing from the megatree, the returned phylogeny portrays a polytomy of genera. - Currently, species are not included in the megatree, and species within a genus are always returned as polytomies. - (http://www.phylodiversity.net/phylomatic/phylomatic_old.html) - - http://bioinformatics.oxfordjournals.org/content/24/18/2098 - Webb, C. O., Ackerly, D. D. and Kembel, S. W. (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics, 24: 2098-2100. - - </help> -</tool> - |
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| diff -r 4de3f9572615 -r 3db16e8335e1 phylomatic/phylomatic_README.txt --- a/phylomatic/phylomatic_README.txt Thu Jun 21 17:46:55 2012 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,50 +0,0 @@ -Phylomatic (Part of Phylocom) - - -http://www.phylodiversity.net/phylomatic/phylomatic.html - - - -"The online software takes your list of taxa, and first tries to match them by genus name to the megatree. - -Failing that, they are attached by family name. If all the genera appear in the megatree, then that family appears resolved. - -If even one genus is missing from the megatree, the returned phylogeny portrays a polytomy of genera. - -Currently, species are not included in the megatree, and species within a genus are always returned as polytomies. - (http://www.phylodiversity.net/phylomatic/phylomatic_old.html) -" -http://bioinformatics.oxfordjournals.org/content/24/18/2098 - - -Webb, C. O., Ackerly, D. D. and Kembel, S. W. (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. - Bioinformatics, 24: 2098-2100. - - -Galaxy and Perl wrapper tool implemented by: Roger Ngo and Todd H. Oakley, UCSB - -Included in this package: - -* phylomatic - binary file -* phylomatic.pl - wrapper perl script for Galaxy -* phylomatic.xml - Galaxy tool file -* phylomatic_README.txt - documentation file - -Installation instruction: - -1. Copy the phylomatic binary file to the /bin/ directory of your Galaxy -user account. - -2. Copy phylomatic.pl and phylomatic.xml to a folder in the /galaxy-dist/tools/ -directory. - -3. Add the XML information in tool_conf.xml in /galaxy-dist/ - -4. Restart Galaxy using: - -./run.sh --stop-daemon -./run.sh --reload --daemon - -Known Issues: -Since Galaxy will throw STDERR on warnings generated by programs, the Perl wrappper -script is used to redirect any warnings generated by the binary file to a log file. \ No newline at end of file |
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| diff -r 4de3f9572615 -r 3db16e8335e1 ucsb_phylogenetics/phylobayes/pb.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ucsb_phylogenetics/phylobayes/pb.pl Thu Jun 21 17:48:46 2012 -0400 |
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| @@ -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; |
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| diff -r 4de3f9572615 -r 3db16e8335e1 ucsb_phylogenetics/phylobayes/pb.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ucsb_phylogenetics/phylobayes/pb.xml Thu Jun 21 17:48:46 2012 -0400 |
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| @@ -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> |
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| diff -r 4de3f9572615 -r 3db16e8335e1 ucsb_phylogenetics/phylobayes/phylobayes_README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ucsb_phylogenetics/phylobayes/phylobayes_README.txt Thu Jun 21 17:48:46 2012 -0400 |
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| @@ -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 |
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| diff -r 4de3f9572615 -r 3db16e8335e1 ucsb_phylogenetics/phylobayes/phylobayes_wrapper.tar.bz2 |
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| Binary file ucsb_phylogenetics/phylobayes/phylobayes_wrapper.tar.bz2 has changed |
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| diff -r 4de3f9572615 -r 3db16e8335e1 ucsb_phylogenetics/phylomatic/phylomatic |
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| Binary file ucsb_phylogenetics/phylomatic/phylomatic has changed |
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| diff -r 4de3f9572615 -r 3db16e8335e1 ucsb_phylogenetics/phylomatic/phylomatic.pl --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ucsb_phylogenetics/phylomatic/phylomatic.pl Thu Jun 21 17:48:46 2012 -0400 |
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| @@ -0,0 +1,10 @@ +#!/usr/bin/perl + +#wrapper written by Roger Ngo and Todd H Oakley, UCSB + +my $file1 = $ARGV[0]; +my $file2 = $ARGV[1]; + +my $run = qx/phylomatic -f $file1 -t $file2 > output.txt 2> errors.txt /; + +print $run; |
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| diff -r 4de3f9572615 -r 3db16e8335e1 ucsb_phylogenetics/phylomatic/phylomatic.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ucsb_phylogenetics/phylomatic/phylomatic.xml Thu Jun 21 17:48:46 2012 -0400 |
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| @@ -0,0 +1,29 @@ +<tool id="phylomatic" name="Phylomatic"> + <description>Run Phylomatic</description> + <command interpreter="perl">./phylomatic.pl $input1 $input2</command> + <inputs> + <param name="input1" type="data" format="txt" label="Phylogenetic Tree" /> + <param name="input2" type="data" format="txt" label="Taxonomy File" /> + </inputs> + + <outputs> + <data from_work_dir="output.txt"/> + </outputs> + + <help> + Phylomatic (Part of Phylocom) + + http://www.phylodiversity.net/phylomatic/phylomatic.html + + The online software takes your list of taxa, and first tries to match them by genus name to the megatree. + Failing that, they are attached by family name. If all the genera appear in the megatree, then that family appears resolved. + If even one genus is missing from the megatree, the returned phylogeny portrays a polytomy of genera. + Currently, species are not included in the megatree, and species within a genus are always returned as polytomies. + (http://www.phylodiversity.net/phylomatic/phylomatic_old.html) + + http://bioinformatics.oxfordjournals.org/content/24/18/2098 + Webb, C. O., Ackerly, D. D. and Kembel, S. W. (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. Bioinformatics, 24: 2098-2100. + + </help> +</tool> + |
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| diff -r 4de3f9572615 -r 3db16e8335e1 ucsb_phylogenetics/phylomatic/phylomatic_README.txt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/ucsb_phylogenetics/phylomatic/phylomatic_README.txt Thu Jun 21 17:48:46 2012 -0400 |
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| @@ -0,0 +1,50 @@ +Phylomatic (Part of Phylocom) + + +http://www.phylodiversity.net/phylomatic/phylomatic.html + + + +"The online software takes your list of taxa, and first tries to match them by genus name to the megatree. + +Failing that, they are attached by family name. If all the genera appear in the megatree, then that family appears resolved. + +If even one genus is missing from the megatree, the returned phylogeny portrays a polytomy of genera. + +Currently, species are not included in the megatree, and species within a genus are always returned as polytomies. + (http://www.phylodiversity.net/phylomatic/phylomatic_old.html) +" +http://bioinformatics.oxfordjournals.org/content/24/18/2098 + + +Webb, C. O., Ackerly, D. D. and Kembel, S. W. (2008) Phylocom: software for the analysis of phylogenetic community structure and trait evolution. + Bioinformatics, 24: 2098-2100. + + +Galaxy and Perl wrapper tool implemented by: Roger Ngo and Todd H. Oakley, UCSB + +Included in this package: + +* phylomatic - binary file +* phylomatic.pl - wrapper perl script for Galaxy +* phylomatic.xml - Galaxy tool file +* phylomatic_README.txt - documentation file + +Installation instruction: + +1. Copy the phylomatic binary file to the /bin/ directory of your Galaxy +user account. + +2. Copy phylomatic.pl and phylomatic.xml to a folder in the /galaxy-dist/tools/ +directory. + +3. Add the XML information in tool_conf.xml in /galaxy-dist/ + +4. Restart Galaxy using: + +./run.sh --stop-daemon +./run.sh --reload --daemon + +Known Issues: +Since Galaxy will throw STDERR on warnings generated by programs, the Perl wrappper +script is used to redirect any warnings generated by the binary file to a log file. \ No newline at end of file |