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comparison tool_dependencies.xml @ 31:7c0d935bd205

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Change tool_dependencies.xml to use package_defuse_0_6_1
author Jim Johnson <jj@umn.edu>
date Tue, 03 Sep 2013 10:59:43 -0500
parents d0f4f4918b78
children 3099cec648e7
comparison
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30:d0f4f4918b78 31:7c0d935bd205
1 <?xml version="1.0"?> 1 <?xml version="1.0"?>
2 <tool_dependency> 2 <tool_dependency>
3 <package name="boost" version="1.53.0"> 3 <package name="defuse" version="0.6.1">
4 <repository changeset_revision="a72f8efe9201" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 4 <repository changeset_revision="370c0672e531" name="package_defuse_0_6_1" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
5 </package> 5 </package>
6 <package name="samtools" version="0.1.18"> 6 <package name="samtools" version="0.1.19">
7 <repository changeset_revision="5f7ec5048224" name="package_samtools_0_1_18" owner="devteam" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 7 <repository changeset_revision="06697b4877f9" name="package_samtools_0_1_19" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
8 </package> 8 </package>
9 <package name="bowtie" version="1.0.0"> 9 <package name="bowtie" version="1.0.0">
10 <repository changeset_revision="e682af6a72cd" name="package_bowtie_1_0_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 10 <repository changeset_revision="e682af6a72cd" name="package_bowtie_1_0_0" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
11 </package> 11 </package>
12 <package name="gmap" version="2013-05-09"> 12 <package name="gmap" version="2013-05-09">
13 <repository changeset_revision="8bacc25e2023" name="package_gmap_2013_05_09" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 13 <repository changeset_revision="8bacc25e2023" name="package_gmap_2013_05_09" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
14 </package> 14 </package>
15 <package name="kent" version="latest"> 15 <package name="kent" version="latest">
16 <repository changeset_revision="b05b788e3989" name="package_kent" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" /> 16 <repository changeset_revision="b05b788e3989" name="package_kent" owner="jjohnson" toolshed="http://testtoolshed.g2.bx.psu.edu" />
17 </package> 17 </package>
18 <package name="defuse" version="0.6.1">
19 <install version="1.0">
20 <actions>
21 <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.6/defuse-0.6.1.tar.gz</action>
22 <!-- populate the environment variables from the dependent repos -->
23 <action type="set_environment_for_install">
24 <repository changeset_revision="a72f8efe9201" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" >
25 <package name="boost" version="1.53.0" />
26 </repository>
27 </action>
28 <action type="shell_command">export CPLUS_INCLUDE_PATH=$BOOST_ROOT_DIR:$CPLUS_INCLUDE_PATH &amp;&amp; cd tools &amp;&amp; make</action>
29 <!-- modify create_reference_dataset.pl to handle more than just human genomes -->
30 <action type="shell_command">
31 cd scripts &amp;&amp;
32 cp create_reference_dataset.pl create_reference_dataset.pl.orig &amp;&amp;
33 cat create_reference_dataset.pl.orig |
34 sed 's#wget_gunzip("ftp://hgdownload.cse.ucsc.edu/goldenPath/$ucsc_genome_version/database/rmsk.txt.gz", $repeats_filename);##' |
35 sed 's#wget_gunzip("ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/intronEst.txt.gz", $est_alignments);##' |
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");#' |
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/' |
38 tr 'Q' '\n' |
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 $0;}' |
40 sed 's#UniGene/Homo_sapiens#UniGene/$ncbi_organism#' |
41 sed 's/Hs.seq.uniq.gz/$ncbi_prefix.seq.uniq.gz/' |
42 sed 's/homo_sapiens/$ensembl_organism/' |
43 sed 's/Homo_sapiens/$ensembl_prefix/' |
44 sed 's/hg19/$ucsc_genome_version/' > create_reference_dataset.pl
45 </action>
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>
53 <action type="set_environment">
54 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/tools</environment_variable>
55 </action>
56 </actions>
57 </install>
58 <readme>
59 deFuse code
60 To build the deFuse toolset you must have the boost c++ development libraries installed. If they are not installed on your system you can download them from the boost website. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, `export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH`)
61 </readme>
62 </package>
63
64 </tool_dependency> 18 </tool_dependency>