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Add breakpoints.bam output derived from breakpoints.genome.psl
author Jim Johnson <jj@umn.edu>
date Tue, 03 Sep 2013 06:41:19 -0500
parents 547d8db4673e
children 103d61bfa1f3
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1 <?xml version="1.0"?>
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2 <tool_dependency>
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3 <package name="boost" version="1.53.0">
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4 <repository changeset_revision="f5b13e56a321" name="package_boost_1_53" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="samtools" version="0.1.18">
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7 <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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8 </package>
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9 <package name="bowtie" version="1.0.0">
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10 <repository changeset_revision="e682af6a72cd" name="package_bowtie_1_0_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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11 </package>
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12 <package name="gmap" version="2013-05-09">
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13 <repository changeset_revision="8bacc25e2023" name="package_gmap_2013_05_09" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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14 </package>
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15 <package name="kent" version="latest">
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16 <repository changeset_revision="b05b788e3989" name="package_kent" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
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17 </package>
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18 <package name="defuse" version="0.6.1">
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19 <install version="1.0">
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20 <actions>
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21 <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.6/defuse-0.6.1.tar.gz</action>
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22 <!-- populate the environment variables from the dependent repos -->
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23 <action type="set_environment_for_install">
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24 <repository changeset_revision="f5b13e56a321" name="package_boost_1_53" owner="bgruening" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" >
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25 <package name="boost" version="1.53.0" />
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26 </repository>
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27 </action>
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28 <action type="shell_command">export CPLUS_INCLUDE_PATH=$BOOST_ROOT_DIR:$CPLUS_INCLUDE_PATH &amp;&amp; cd tools &amp;&amp; make</action>
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29 <!-- modify create_reference_dataset.pl to handle more than just human genomes -->
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30 <action type="shell_command">
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31 cd scripts &amp;&amp;
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32 cp create_reference_dataset.pl create_reference_dataset.pl.orig &amp;&amp;
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33 cat create_reference_dataset.pl.orig |
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34 sed 's#wget_gunzip("ftp://hgdownload.cse.ucsc.edu/goldenPath/$ucsc_genome_version/database/rmsk.txt.gz", $repeats_filename);##' |
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35 sed 's#wget_gunzip("ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/intronEst.txt.gz", $est_alignments);##' |
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36 sed 's#^\(my .*ensembl_genome_version.*config.*get_value.*;\)#\1Qmy $ensembl_organism = $config->get_value("ensembl_organism");Qmy $ensembl_prefix = $config->get_value("ensembl_prefix");Qmy $ncbi_organism = $config->get_value("ncbi_organism");Qmy $ncbi_prefix = $config->get_value("ncbi_prefix");#' |
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37 sed 's/^\(sub wget_gunzip\)/sub try_wgetQ{Q my $url = shift;Q my $filename = shift;Q my $filename_gz = $filename.".gz";Q my $rslt = system "wget $url -O $filename_gz";Q if($rslt == 0)Q {Q $rslt = system "gunzip $filename_gz";Q }Q return $rslt;Q}QQ\1/' |
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38 tr 'Q' '\n' |
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39 awk 'BEGIN{pfx="p1";fn="p2";}/if \(not -e \$repeats_filename\)/{pfx="rmsk";fn="repeats_filename";} /if \(not -e \$est_alignments\)/{pfx="intronEst";fn="est_alignments"} /ucsc_genome_version eq "hg18"/{printf("\tif (try_wget(\"ftp://hgdownload.cse.ucsc.edu/goldenPath/$ucsc_genome_version/database/%s.txt.gz\", \$%s) != 0)\n",pfx,fn);} $0 !~ /ucsc_genome_version eq "hg18/{print $0;}' |
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40 sed 's#UniGene/Homo_sapiens#UniGene/$ncbi_organism#' |
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41 sed 's/Hs.seq.uniq.gz/$ncbi_prefix.seq.uniq.gz/' |
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42 sed 's/homo_sapiens/$ensembl_organism/' |
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43 sed 's/Homo_sapiens/$ensembl_prefix/' |
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44 sed 's/hg19/$ucsc_genome_version/' > create_reference_dataset.pl
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45 </action>
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46 <action type="move_directory_files">
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47 <source_directory>.</source_directory>
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48 <destination_directory>$INSTALL_DIR</destination_directory>
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49 </action>
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50 <action type="set_environment">
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51 <environment_variable name="DEFUSE_PATH" action="set_to">$INSTALL_DIR</environment_variable>
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52 </action>
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53 <action type="set_environment">
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54 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/tools</environment_variable>
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55 </action>
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56 </actions>
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57 </install>
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58 <readme>
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59 deFuse code
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60 To build the deFuse toolset you must have the boost c++ development libraries installed. If they are not installed on your system you can download them from the boost website. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, `export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH`)
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61 </readme>
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62 </package>
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64 </tool_dependency>