Changes between Initial Version and Version 1 of cypress/WGSA

Timestamp:

07/14/20 14:29:49 (5 years ago)

Author:

fuji

Comment:

—

cypress/WGSA

@@ +1 @@
+[[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
+}}}
+
+