Mercurial > repos > jjohnson > package_defuse_0_6_2
comparison tool_dependencies.xml @ 0:5a4237bbe6bf draft
planemo upload for repository https://github.com/jj-umn/galaxytools/tree/master/packages/package_defuse_0_6_2 commit e9b93500b3fd7b26de9b8218b63d8346c6682634-dirty
author | jjohnson |
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date | Sun, 17 Jan 2016 13:03:12 -0500 |
parents | |
children | 8bfe32e9a29b |
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1 <?xml version="1.0"?> | |
2 <tool_dependency> | |
3 <package name="boost" version="1.53.0"> | |
4 <repository changeset_revision="53dae122c9c7" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" /> | |
5 </package> | |
6 <package name="defuse" version="0.6.2"> | |
7 <install version="1.0"> | |
8 <actions> | |
9 <action type="shell_command">git clone https://bitbucket.org/dranew/defuse.git defuse</action> | |
10 <action type="shell_command">git reset --hard 5c13b80f62bcbb8ac4b7d517488be0986b080723</action> | |
11 <!-- populate the environment variables from the dependent repos --> | |
12 <action type="set_environment_for_install"> | |
13 <repository changeset_revision="53dae122c9c7" name="package_boost_1_53" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu"> | |
14 <package name="boost" version="1.53.0" /> | |
15 </repository> | |
16 </action> | |
17 <action type="shell_command">export CPLUS_INCLUDE_PATH=$BOOST_ROOT_DIR/include:$CPLUS_INCLUDE_PATH && cd tools && make</action> | |
18 <!-- modify create_reference_dataset.pl to handle more than just human genomes --> | |
19 <action type="shell_command"> | |
20 cd scripts && | |
21 cp create_reference_dataset.pl create_reference_dataset.pl.orig && | |
22 cat create_reference_dataset.pl.orig | | |
23 sed 's#wget_gunzip("ftp://hgdownload.cse.ucsc.edu/goldenPath/$ucsc_genome_version/database/rmsk.txt.gz", $repeats_filename);##' | | |
24 sed 's#wget_gunzip("ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/intronEst.txt.gz", $est_alignments);##' | | |
25 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");#' | | |
26 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/' | | |
27 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");#' | | |
28 tr 'Q' '\n' | | |
29 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 $0;}' | | |
30 sed 's#UniGene/Homo_sapiens#UniGene/$ncbi_organism#' | | |
31 sed 's/Hs.seq.uniq.gz/$ncbi_prefix.seq.uniq.gz/' | | |
32 sed 's/homo_sapiens/$ensembl_organism/' | | |
33 sed 's/Homo_sapiens/$ensembl_prefix/' | | |
34 sed 's/hg19/$ucsc_genome_version/' > create_reference_dataset.pl | |
35 </action> | |
36 <action type="move_directory_files"> | |
37 <source_directory>.</source_directory> | |
38 <destination_directory>$INSTALL_DIR</destination_directory> | |
39 </action> | |
40 <action type="set_environment"> | |
41 <environment_variable action="set_to" name="DEFUSE_PATH">$INSTALL_DIR</environment_variable> | |
42 </action> | |
43 <action type="set_environment"> | |
44 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tools</environment_variable> | |
45 </action> | |
46 </actions> | |
47 </install> | |
48 <readme> | |
49 deFuse code | |
50 To build the deFuse toolset you must have the boost c++ development libraries installed. If they are not installed on your system you can download them from the boost website. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, `export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH`) | |
51 </readme> | |
52 </package> | |
53 | |
54 </tool_dependency> |