Install¶
WOLAND is a multiplatform tool based on Perl and R. Please observe prerequisites and modules and libraries need. They must be installed before WOLAND installation.
Prerequisites¶
The following software must be present before installing Woland:
Perl (Minimal recommended Perl version: 5.17)¶
To check Perl version type:
$ perl -v
The following Perl modules should be present:
- Bio::DB::Fasta
- Cwd
- List::Util
- IPC::System::Simple
- IPC::Run
- Parallel::ForkManager
- Regexp::Common
- Text::Balanced(>=1.97)
- Text::Wrap
- Statistics::R
R (Minimal recommended R version: 3.1)¶
To check R version type (in R):
$ R.Version()
The following R packages must be installed:
- plyr
- reshape2
- ggplot2
- qqman
- RColorBrewer
Installation¶
Installing Perl modules¶
You can use CPAN to get any missing module. First install cpanm:
$ sudo cpan App::cpanminus
Them you can install each module:
$ sudo cpanm Module::Name
Installing R packages¶
You can use this following command in R to install each missing library:
$R install.packages(packagename)
Installing source WOLAND files¶
Download last Woland source release in <link>. Woland is provided as a tar.gz file which could be extracted using, for example:
$ tar -xvzf woland-<version>-install.tar.gz
Woland will be installed inside woland installation folder install_dir.
Copying genome sequences and annotation¶
Woland needs genome reference sequence and its gene annotation for each organism in the $install_dir/genomes folder. User should download two files in order to perform its analysis:
Note
These files can be downloaded using UCSC database (http://hgdownload.cse.ucsc.edu/downloads.html). See below how to rename them:
$install_dir/genomes/genome_<genome_version>.fa
$install_dir/genomes/refseq_<genome_version>.txt
Warning
You must rename <genome_version>.fa and refGene.txt according to <genome_version>.
For example:
hg19:
$install_dir/genomes/genome_hg19.fa $install_dir/genomes/refseq_hg19.fa
mm10:
$install_dir/genomes/genome_mm10.fa $install_dir/genomes/refseq_mm10.fa