[[PageOutline]]
= Installing and Setup WGSA in a local directory on Cypress =
Decide a folder dedicated for the pipeline, for example '/lustre/project/group/WGSA'.

Setup an environment variable and create workspaces as
{{{
export $WGSA_DIR=/lustre/project/group/WGSA
mkdir $WGSA_DIR
cd $WGSA_DIR
mkdir work
mkdir tmp
chmod 777 work
chmod 777 tmp
}}}

Create a space for ANNOVAR,

{{{
mkdir $WGSA_DIR/annovar
}}}


Download the ANNOVAR main package from [http://download.openbioinformatics.org/annovar_download_form.php here].
The package comes as annovar.latest.tar.gz, save it to $WGSA_DIR/annovar. Unzip it.


{{{
cd $WGSA_DIR/annovar
tar -zxvf annovar.latest.tar.gz
}}}

Download !RefSeq and !Ensembl gene models for ANNOVAR:

{{{
cd $WGSA_DIR/annovar/annovar
perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar refGene humandb/
perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar ensGene humandb/
perl annotate_variation.pl -buildver hg19 -downdb -webfrom annovar knownGene humandb/
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar refGene humandb/
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar ensGene humandb/     
perl annotate_variation.pl -buildver hg38 -downdb -webfrom annovar knownGene humandb/    
}}}

Install !SnpEff (required for annotating indels with !SnpEff or annotating SNVs with !SnpEff on-the-fly)
Download !SnpEff v4.3t main package and save the zip file to $WGSA_DIR/snpeff:

{{{
mkdir $WGSA_DIR/snpeff
cd $WGSA_DIR/snpeff
wget http://sourceforge.net/projects/snpeff/files/snpEff_v4_3t_core.zip
unzip snpEff_v4_3t_core.zip
}}}

Now you need a newer version of JavaSDK, to use it, you have to do on a computing node.

Start a interactive session:

{{{
idev
}}}

See [https://wiki.hpc.tulane.edu/trac/wiki/Workshops/IntroToHpc2015/using#SubmittingInteractiveJobs here] for more about 'idev'.

Once you get to a computing node, make sure your corrent directory is $WGSA_DIR/snpeff

Download !RefSeq and !Ensembl gene models for !SnpEff:

{{{
cd snpEff
java -jar snpEff.jar download -v hg19
java -jar snpEff.jar download -v GRCh37.75
java -jar snpEff.jar download -v hg38
java -jar snpEff.jar download -v GRCh38.86
}}}

Exit from the computing node:

{{{
exit
}}}

Install VEP (required for annotating indels with VEP or annotating SNVs with VEP on-the-fly)

Download VEP 94 main package and save it to $WGSA_DIR/vep:

{{{
mkdir $WGSA_DIR/vep
cd $WGSA_DIR/vep
wget https://github.com/Ensembl/ensembl-vep/archive/release/94.zip
unzip 94.zip
}}}