Mercurial > repos > jjohnson > package_defuse_0_6_2

comparison tool_dependencies.xml @ 0:bf5636f162fe draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author jjohnson
date Mon, 04 Jan 2016 14:13:24 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:bf5636f162fe
1 <?xml version="1.0"?>
2 <tool_dependency>
3 <package name="boost" version="1.53.0">
4 <repository changeset_revision="a534981960ca" name="package_boost_1_53" owner="iuc" prior_installation_required="True" toolshed="https://testtoolshed.g2.bx.psu.edu" />
5 </package>
6 <package name="defuse" version="0.6.2">
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">
12 <repository changeset_revision="a534981960ca" name="package_boost_1_53" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
13 <package name="boost" version="1.53.0" />
14 </repository>
15 </action>
16 <action type="shell_command">export CPLUS_INCLUDE_PATH=$BOOST_ROOT_DIR/include:$CPLUS_INCLUDE_PATH &amp;&amp; cd tools &amp;&amp; make</action>
17 <!-- modify create_reference_dataset.pl to handle more than just human genomes -->
18 <action type="shell_command">
19 cd scripts &amp;&amp;
20 cp create_reference_dataset.pl create_reference_dataset.pl.orig &amp;&amp;
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-&gt;get_value("ensembl_organism");Qmy $ensembl_prefix = $config-&gt;get_value("ensembl_prefix");Qmy $ncbi_organism = $config-&gt;get_value("ncbi_organism");Qmy $ncbi_prefix = $config-&gt;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/' |
26 sed 's#^\(.*/gtf/.*\)$#\1Q system_with_check("if `grep -v gene_name $gene_models &gt; /dev/null`; then mv $gene_models ${gene_models}.orig; grep gene_name ${gene_models}.orig &gt; $gene_models; fi");#' |
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/' &gt; create_reference_dataset.pl
34 </action>
35 <action type="move_directory_files">
36 <source_directory>.</source_directory>
37 <destination_directory>$INSTALL_DIR</destination_directory>
38 </action>
39 <action type="set_environment">
40 <environment_variable action="set_to" name="DEFUSE_PATH">$INSTALL_DIR</environment_variable>
41 </action>
42 <action type="set_environment">
43 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/tools</environment_variable>
44 </action>
45 </actions>
46 </install>
47 <readme>
48 deFuse code
49 To build the deFuse toolset you must have the boost c++ development libraries installed. If they are not installed on your system you can download them from the boost website. A full install of boost is not required. The easiest thing to do is to download the latest boost source tar.gz, extract it, then add the extracted path to the CPLUS_INCLUDE_PATH environment variable (in bash, `export CPLUS_INCLUDE_PATH=/boost/directory/:$CPLUS_INCLUDE_PATH`)
50 </readme>
51 </package>
52
53 </tool_dependency>