Mercurial > repos > elixir-it > covacs_annovar

view dwl_autom_from_wrapper.sh @ 3:714413403c9a draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author elixir-it
date Wed, 02 Oct 2019 04:32:16 -0400
parents ab0933ba7535
children
line wrap: on
line source

#/bin/bash
#bash script to download autamatically from the wrapper the database of annovar
echo start &&
perl $CONDA_PREFIX/../../annovar/annotate_variation.pl  -downdb -buildver hg19 -webfrom annovar gnomad_genome $CONDA_PREFIX/../../annovar/humandb &&
perl $CONDA_PREFIX/../../annovar/annotate_variation.pl  -downdb -buildver hg19 -webfrom annovar exac03 $CONDA_PREFIX/../../annovar/humandb &&
perl $CONDA_PREFIX/../../annovar/annotate_variation.pl  -downdb -buildver hg19 -webfrom annovar 1000g2015aug $CONDA_PREFIX/../../annovar/humandb &&
perl $CONDA_PREFIX/../../annovar/annotate_variation.pl  -downdb -buildver hg19 -webfrom annovar avsnp150 $CONDA_PREFIX/../../annovar/humandb &&
perl $CONDA_PREFIX/../../annovar/annotate_variation.pl  -downdb -buildver hg19 -webfrom annovar clinvar_20180603 $CONDA_PREFIX/../../annovar/humandb &&
perl $CONDA_PREFIX/../../annovar/annotate_variation.pl  -downdb -buildver hg19 -webfrom annovar cosmic70 $CONDA_PREFIX/../../annovar/humandb &&
perl $CONDA_PREFIX/../../annovar/annotate_variation.pl  -downdb -buildver hg19 -webfrom annovar dbnsfp33a $CONDA_PREFIX/../../annovar/humandb &&
perl $CONDA_PREFIX/../../annovar/annotate_variation.pl  -downdb -buildver hg19 -webfrom annovar esp6500_all $CONDA_PREFIX/../../annovar/humandb &&
perl $CONDA_PREFIX/../../annovar/annotate_variation.pl  -downdb -buildver hg19 -webfrom annovar kaviar_20150923 $CONDA_PREFIX/../../annovar/humandb &&
perl $CONDA_PREFIX/../../annovar/annotate_variation.pl  -downdb -buildver hg19 -webfrom annovar knownGene $CONDA_PREFIX/../../annovar/humandb &&
perl $CONDA_PREFIX/../../annovar/annotate_variation.pl  -downdb -buildver hg19 -webfrom annovar mitimpact2 $CONDA_PREFIX/../../annovar/humandb &&
perl $CONDA_PREFIX/../../annovar/annotate_variation.pl  -downdb -buildver hg19 -webfrom annovar refGene $CONDA_PREFIX/../../annovar/humandb &&
echo end