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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="a534981960ca" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
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5 </package>
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6 <package name="defuse" version="0.6.2">
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7 <install version="1.0">
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8 <actions>
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9 <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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10 <!-- populate the environment variables from the dependent repos -->
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11 <action type="set_environment_for_install">
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12 <repository changeset_revision="a534981960ca" name="package_boost_1_53" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
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13 <package name="boost" version="1.53.0" />
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14 </repository>
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15 </action>
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16 <action type="shell_command">export CPLUS_INCLUDE_PATH=$BOOST_ROOT_DIR/include:$CPLUS_INCLUDE_PATH && cd tools && make</action>
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17 <!-- modify create_reference_dataset.pl to handle more than just human genomes -->
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18 <action type="shell_command">
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19 cd scripts &&
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20 cp create_reference_dataset.pl create_reference_dataset.pl.orig &&
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21 cat create_reference_dataset.pl.orig |
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22 sed 's#wget_gunzip("ftp://hgdownload.cse.ucsc.edu/goldenPath/$ucsc_genome_version/database/rmsk.txt.gz", $repeats_filename);##' |
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23 sed 's#wget_gunzip("ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/intronEst.txt.gz", $est_alignments);##' |
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24 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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25 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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26 sed 's#^\(.*/gtf/.*\)$#\1Q system_with_check("if `grep -v gene_name $gene_models > /dev/null`; then mv $gene_models ${gene_models}.orig; grep gene_name ${gene_models}.orig > $gene_models; fi");#' |
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27 tr 'Q' '\n' |
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28 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 $0;}' |
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29 sed 's#UniGene/Homo_sapiens#UniGene/$ncbi_organism#' |
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30 sed 's/Hs.seq.uniq.gz/$ncbi_prefix.seq.uniq.gz/' |
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31 sed 's/homo_sapiens/$ensembl_organism/' |
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32 sed 's/Homo_sapiens/$ensembl_prefix/' |
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33 sed 's/hg19/$ucsc_genome_version/' > create_reference_dataset.pl
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34 </action>
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35 <action type="move_directory_files">
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36 <source_directory>.</source_directory>
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37 <destination_directory>$INSTALL_DIR</destination_directory>
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38 </action>
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39 <action type="set_environment">
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40 <environment_variable action="set_to" name="DEFUSE_PATH">$INSTALL_DIR</environment_variable>
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41 </action>
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42 <action type="set_environment">
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43 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tools</environment_variable>
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44 </action>
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45 </actions>
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46 </install>
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47 <readme>
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48 deFuse code
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49 To build the deFuse toolset you must have the boost c++ development libraries installed. If they are not installed on your system you can download them from the boost website. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, `export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH`)
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50 </readme>
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51 </package>
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52
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53 </tool_dependency>
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