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annotate phylogenies/phylobayes33_wrapper.pl @ 0:5b9a38ec4a39 draft default tip

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First commit of old repositories
author osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
date Tue, 11 Mar 2014 12:19:13 -0700
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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1 #!/usr/bin/perl
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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2
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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3 my $phylobayes_path = '/home/galaxy/pkgs/phylobayes3.3b/exe_lin64/pb';
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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4 my $readPB_path = '/home/galaxy/pkgs/phylobayes3.3b/exe_lin64/readpb';
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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5
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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6 my $fileName = $ARGV[0];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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7 my $nchainInput = $ARGV[1];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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8 my $cycle_bp_trace_comp = $ARGV[2];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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9 my $discrepancies_threshold = $ARGV[3];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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10 my $effective_size_floor = $ARGV[4];
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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11 my $jobName = "dataset";
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12
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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13 my $burnin = $ARGV[5];
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14 my $sampleInterval = $ARGV[6];
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15
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16 my $run1 = qx/$phylobayes_path -d $fileName -nchain $nchainInput $cycle_bp_trace_comp $discrepancies_threshold $effective_size_floor $jobName 2>errorlog/;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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17 print $run1;
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18
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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19 my $list = qx/ls -l/;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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20 print $list;
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21
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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22 my $run2 = qx/$readPB_path -x $burnin $sampleInterval $jobName 2>errorlog/;
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osiris_phylogenetics <ucsb_phylogenetics@lifesci.ucsb.edu>
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23 print $run2;