Mercurial > repos > elixir-it > covacs_annovar

changeset 1:ab0933ba7535 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author elixir-it
date Thu, 15 Nov 2018 15:48:25 -0500
parents a28564bf926a
children 40db0c5e3310
files dwl_autom_from_wrapper.sh dwl_db_annovar_terminal.sh tool-data/annovar.loc.sample
diffstat 3 files changed, 37 insertions(+), 6 deletions(-) [+]
line wrap: on
line diff
--- /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
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/dwl_db_annovar_terminal.sh	Thu Nov 15 15:48:25 2018 -0500
@@ -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
--- 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
@@ -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