Mercurial > repos > jjohnson > package_defuse_0_6_1
annotate tool_dependencies.xml @ 2:252b7103d152 default tip
Change for prior_installation_required
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Wed, 16 Oct 2013 07:30:37 -0500 |
| parents | 66cb7175c473 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 3 <package name="boost" version="1.53.0"> | |
| 4 <repository changeset_revision="a72f8efe9201" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="http://testtoolshed.g2.bx.psu.edu" /> | |
| 5 </package> | |
| 6 <package name="defuse" version="0.6.1"> | |
| 7 <install version="1.0"> | |
| 8 <actions> | |
| 9 <action type="download_by_url">http://sourceforge.net/projects/defuse/files/defuse/0.6/defuse-0.6.1.tar.gz</action> | |
| 10 <!-- populate the environment variables from the dependent repos --> | |
| 11 <action type="set_environment_for_install"> | |
|
2
252b7103d152
Change for prior_installation_required
Jim Johnson <jj@umn.edu>
parents:
1
diff
changeset
|
12 <repository changeset_revision="a72f8efe9201" name="package_boost_1_53" owner="iuc" toolshed="http://testtoolshed.g2.bx.psu.edu" > |
| 0 | 13 <package name="boost" version="1.53.0" /> |
| 14 </repository> | |
| 15 </action> | |
| 16 <action type="shell_command">export CPLUS_INCLUDE_PATH=$BOOST_ROOT_DIR:$CPLUS_INCLUDE_PATH && cd tools && make</action> | |
| 17 <!-- modify create_reference_dataset.pl to handle more than just human genomes --> | |
| 18 <action type="shell_command"> | |
| 19 cd scripts && | |
| 20 cp create_reference_dataset.pl create_reference_dataset.pl.orig && | |
| 21 cat create_reference_dataset.pl.orig | | |
| 22 sed 's#wget_gunzip("ftp://hgdownload.cse.ucsc.edu/goldenPath/$ucsc_genome_version/database/rmsk.txt.gz", $repeats_filename);##' | | |
| 23 sed 's#wget_gunzip("ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/intronEst.txt.gz", $est_alignments);##' | | |
| 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");#' | | |
| 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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1
66cb7175c473
Modify defuse create_reference_dataset.pl to filter out GTF lines that do not have a gene_name property, needed for CanFam3.1
Jim Johnson <jj@umn.edu>
parents:
0
diff
changeset
|
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");#' | |
| 0 | 27 tr 'Q' '\n' | |
| 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 $0;}' | | |
| 29 sed 's#UniGene/Homo_sapiens#UniGene/$ncbi_organism#' | | |
| 30 sed 's/Hs.seq.uniq.gz/$ncbi_prefix.seq.uniq.gz/' | | |
| 31 sed 's/homo_sapiens/$ensembl_organism/' | | |
| 32 sed 's/Homo_sapiens/$ensembl_prefix/' | | |
| 33 sed 's/hg19/$ucsc_genome_version/' > create_reference_dataset.pl | |
| 34 </action> | |
| 35 <action type="move_directory_files"> | |
| 36 <source_directory>.</source_directory> | |
| 37 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 38 </action> | |
| 39 <action type="set_environment"> | |
| 40 <environment_variable name="DEFUSE_PATH" action="set_to">$INSTALL_DIR</environment_variable> | |
| 41 </action> | |
| 42 <action type="set_environment"> | |
| 43 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/tools</environment_variable> | |
| 44 </action> | |
| 45 </actions> | |
| 46 </install> | |
| 47 <readme> | |
| 48 deFuse code | |
| 49 To build the deFuse toolset you must have the boost c++ development libraries installed. If they are not installed on your system you can download them from the boost website. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, `export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH`) | |
| 50 </readme> | |
| 51 </package> | |
| 52 | |
| 53 </tool_dependency> |