Commit 9a46c853 authored by Monika Komorowska's avatar Monika Komorowska
Browse files

added cshell script to generate commands for running LRGs

parent 63010ae9
......@@ -119,6 +119,34 @@ perl scripts/ -verbose -do_all -host ens-staging -port
homo_sapiens_cdna_65_37 -vega homo_sapiens_vega_65_37 -rnaseq
homo_sapiens_rnaseq_65_37 -verify >& verify.OUT
c shell script to generate the commands:
set db_args = '-host ens-staging -port 3306 -user ensadmin -pass ensembl'
#delete cdna if it's not ready yet, LRGs will be imported into cdna from core
set db_types =(core otherfeatures vega rnaseq cdna)
set species = 'homo_sapiens'
set dbs = ''
set options = (clean import overlap verify)
set version = '66_37'
foreach type ($db_types)
set dbs = "${dbs} -${type} ${species}_${type}_${version}"
foreach option ($options)
if ($option == 'import') then
set command_line_args = "$db_args $dbs -$option -xrefs"
set command_line_args = "$db_args $dbs -$option "
echo "perl scripts/ -verbose -do_all $command_line_args >& $option.OUT"
If the cdna databases are not yet ready then remove the "-cdna
homo_sapiens_cdna_65_37" bit and continue but let who ever is building
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