[[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
}}}

To use a newer version of JavaSDK, you have to login to 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:

{{{
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:

{{{
exit
}}}

Install htslib, which is required for VEP API.

{{{
mkdir $WGSA_DIR/htslib
cd $WGSA_DIR/htslib
wget https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2
tar -vxjf htslib-1.9.tar.bz2
cd htslib-1.9
make prefix=$WGSA_DIR/htslib install
}}}

Setup the environmental variables

{{{
export PATH=$WGSA_DIR/htslib/bin:$PATH
export CPATH=$WGSA_DIR/htslib/include:$CPATH
export LD_LIBRARY_PATH=$WGSA_DIR/htslib/lib:$LD_LIBRARY_PATH
}}}


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
}}}

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 $WGSA_DIR/.vep
export DEST_DIR=$WGSA_DIR
export PERL5LIB=$WGSA_DIR
perl INSTALL.pl -c $WGSA_DIR/.vep --ASSEMBLY GRCh37
}}}
Go through the steps of the installing process and following the guidance at http://useast.ensembl.org/info/docs/tools/vep/script/vep_tutorial.html. 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 INSTALL.pl -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
wget https://github.com/konradjk/loftee/archive/v0.1.1-beta.zip
unzip -j v0.1.1-beta.zip
rm v0.1.1-beta.zip
}}}