Mercurial > repos > ucsb-phylogenetics > ucsb_phylogenetics

changeset 3:3db16e8335e1 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Phylomatic and Phylobayes included
author ucsb-phylogenetics
date Thu, 21 Jun 2012 17:48:46 -0400
parents 4de3f9572615
children 5b23f3eb3f09
files phylomatic/phylomatic phylomatic/phylomatic.pl phylomatic/phylomatic.xml phylomatic/phylomatic_README.txt 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
diffstat 12 files changed, 237 insertions(+), 89 deletions(-) [+]
line wrap: on
line diff
Binary file phylomatic/phylomatic has changed
--- a/phylomatic/phylomatic.pl	Thu Jun 21 17:46:55 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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;
--- a/phylomatic/phylomatic.xml	Thu Jun 21 17:46:55 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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>
-
--- a/phylomatic/phylomatic_README.txt	Thu Jun 21 17:46:55 2012 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ucsb_phylogenetics/phylobayes/pb.pl	Thu Jun 21 17:48:46 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/ucsb_phylogenetics/phylobayes/pb.xml	Thu Jun 21 17:48:46 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/ucsb_phylogenetics/phylobayes/phylobayes_README.txt	Thu Jun 21 17:48:46 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
\ No newline at end of file
Binary file ucsb_phylogenetics/phylobayes/phylobayes_wrapper.tar.bz2 has changed
Binary file ucsb_phylogenetics/phylomatic/phylomatic has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ucsb_phylogenetics/phylomatic/phylomatic.pl	Thu Jun 21 17:48:46 2012 -0400
@@ -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;
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ucsb_phylogenetics/phylomatic/phylomatic.xml	Thu Jun 21 17:48:46 2012 -0400
@@ -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>
+
--- /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
@@ -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