Mercurial > repos > elixir-it > covacs_annovar

diff dwl_autom_from_wrapper.sh @ 1:ab0933ba7535 draft

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author elixir-it
date Thu, 15 Nov 2018 15:48:25 -0500
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dwl_autom_from_wrapper.sh	Thu Nov 15 15:48:25 2018 -0500
@@ -0,0 +1,16 @@
+#/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