[[PageOutline]] = Installing and Setup WGSA in a local directory on Cypress = This instruction is based on [https://sites.google.com/site/jpopgen/wgsa/setting-up-wgsa-linux this] page and adapted for 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/annovar2019Oct24 }}} 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/annovar2019Oct24. Unzip it. {{{ cd $WGSA_DIR/annovar2019Oct24 tar -zxvf annovar.latest.tar.gz }}} Download !RefSeq and Ensembl gene models for ANNOVAR: {{{ cd $WGSA_DIR/annovar2019Oct24/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 -c 1 -t 4 }}} It will take more than one hour. 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. *This takes very long time... {{{ 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. *This takes very long time... Change the permissions for these directories... {{{ 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 }}} == Download the pipeline programs and other resources == {{{ mkdir $WGSA_DIR/resources cd $WGSA_DIR/resources wget http://web.corral.tacc.utexas.edu/WGSAdownload/resources/javaclass/ --recursive --continue --timestamping --no-host-directories --cut-dirs=2 --no-parent --reject="index.html*" wget http://web.corral.tacc.utexas.edu/WGSAdownload/resources/hg19/ --recursive --continue --timestamping --no-host-directories --cut-dirs=2 --no-parent --reject="index.html*" wget http://web.corral.tacc.utexas.edu/WGSAdownload/resources/hg38/ --recursive --continue --timestamping --no-host-directories --cut-dirs=2 --no-parent --reject="index.html*" }}}