| Previous changeset 0:a28564bf926a (2018-11-08) Next changeset 2:40db0c5e3310 (2018-11-21) |
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Commit message:
Uploaded |
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modified:
tool-data/annovar.loc.sample |
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added:
dwl_autom_from_wrapper.sh dwl_db_annovar_terminal.sh |
| b |
| diff -r a28564bf926a -r ab0933ba7535 dwl_autom_from_wrapper.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dwl_autom_from_wrapper.sh Thu Nov 15 15:48:25 2018 -0500 |
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| @@ -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 |
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| diff -r a28564bf926a -r ab0933ba7535 dwl_db_annovar_terminal.sh --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/dwl_db_annovar_terminal.sh Thu Nov 15 15:48:25 2018 -0500 |
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| @@ -0,0 +1,16 @@ +#/bin/bash +#bash script to download from the terminal the database of annovar launch in /annovar +echo start && +perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar gnomad_genome humandb && +perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar exac03 humandb && +perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar 1000g2015aug humandb && +perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar avsnp150 humandb && +perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar clinvar_20180603 humandb && +perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar cosmic70 humandb && +perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar dbnsfp33a humandb && +perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar esp6500_all humandb && +perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar kaviar_20150923 humandb && +perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar knownGene humandb && +perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar mitimpact2 humandb && +perl annotate_variation.pl -downdb -buildver hg19 -webfrom annovar refGene humandb && +echo end |
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| diff -r a28564bf926a -r ab0933ba7535 tool-data/annovar.loc.sample --- a/tool-data/annovar.loc.sample Thu Nov 08 12:13:56 2018 -0500 +++ b/tool-data/annovar.loc.sample Thu Nov 15 15:48:25 2018 -0500 |
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| @@ -1,10 +1,9 @@ #location of humandb the fields are tab delimited -db location /export/_conda/annovar/humandb +#db location /export/_conda/annovar/humandb - -#definition of present db name + type(gene_ann, region, filter) the fields are tab delimited -refGene gene_ann -prova gene_ann -exac03 filter +#definition of present db name + type(gene_ann, region, filter ) + assembly of the genome the fields are tab delimited +#refGene gene_ann hg19 +#prova gene_ann hg19 +#exac03 filter hg19 |