Version 3 (modified by fuji, 18 months ago) (diff)

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
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 -buildver hg19 -downdb -webfrom annovar refGene humandb/
perl -buildver hg19 -downdb -webfrom annovar ensGene humandb/
perl -buildver hg19 -downdb -webfrom annovar knownGene humandb/
perl -buildver hg38 -downdb -webfrom annovar refGene humandb/
perl -buildver hg38 -downdb -webfrom annovar ensGene humandb/     
perl -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

To use a newer version of JavaSDK, you have to login to a computing node.

Start a interactive session:


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:

module load java-openjdk/1.8.0
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:


Install htslib, which is required for VEP API.

mkdir $WGSA_DIR/htslib
cd $WGSA_DIR/htslib
tar -vxjf htslib-1.9.tar.bz2
cd htslib-1.9
make prefix=$WGSA_DIR/htslib install

Setup the environmental variables

export PATH=$WGSA_DIR/htslib/bin:$PATH
export CPATH=$WGSA_DIR/htslib/include:$CPATH

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

Install VEP API to /WGSA/vep and download RefSeq and Ensembl gene models to $WGSA_DIR/.vep

cd $WGSA_DIR/vep/ensembl-vep-release-94/
mkdir $WGSA_DIR/.vep
perl -c $WGSA_DIR/.vep --ASSEMBLY GRCh37

Go through the steps of the installing process and following the guidance at When being asked for the cache files, choose “242 : homo_sapiens_merged_vep_94_GRCh37.tar.gz”. When being asked for fasta files, choose “27 : homo_sapiens”. When being asked for the plugins, choose "7:LOF". The fasta file downloading is required for the current version of WGSA.

perl -c $WGSA_DIR/.vep --ASSEMBLY GRCh38

When being asked for the cache files, choose "243 : homo_sapiens_merged_vep_94_GRCh38.tar.gz". When being asked for fasta files, choose “54: homo_sapiens”. When being asked for the plugins, choose "n" as LOF has already been installed.

chmod 777 $WGSA_DIR/.vep/Plugins
chmod 777 $WGSA_DIR/.vep/homo_sapiens/94_GRCh37
chmod 777 $WGSA_DIR/.vep/homo_sapiens/94_GRCh38

Install LOFTEE LOF plugin for VEP API

cd $WGSA_DIR/.vep/Plugins
unzip -j