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 ​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 ​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