Mercurial > repos > jjohnson > defuse
annotate tool_dependencies.xml @ 22:68494d6aabeb
Update datamanager and defuse.xml config file generation
author | Jim Johnson <jj@umn.edu> |
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date | Thu, 27 Jun 2013 13:11:50 -0500 |
parents | 547d8db4673e |
children | 103d61bfa1f3 |
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0 | 1 <?xml version="1.0"?> |
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"> |
11 | 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"> |
0 | 19 <install version="1.0"> |
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 && cd tools && 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 && |
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32 cp create_reference_dataset.pl create_reference_dataset.pl.orig && |
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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> |
0 | 46 <action type="move_directory_files"> |
47 <source_directory>.</source_directory> | |
48 <destination_directory>$INSTALL_DIR</destination_directory> | |
49 </action> | |
50 <action type="set_environment"> | |
51 <environment_variable name="DEFUSE_PATH" action="set_to">$INSTALL_DIR</environment_variable> | |
52 </action> | |
16 | 53 <action type="set_environment"> |
54 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/tools</environment_variable> | |
55 </action> | |
0 | 56 </actions> |
57 </install> | |
58 <readme> | |
6 | 59 deFuse code |
60 To build the deFuse toolset you must have the boost c++ development libraries installed. If they are not installed on your system you can download them from the boost website. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, `export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH`) | |
0 | 61 </readme> |
62 </package> | |
63 | |
64 </tool_dependency> |