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Input full path to cache directory #1707

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Jul 17, 2024
Merged

Input full path to cache directory #1707

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4 changes: 3 additions & 1 deletion modules/Bio/EnsEMBL/VEP/CacheDir.pm
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Expand Up @@ -104,7 +104,9 @@ sub new {

# need to either specify full path (dir) e.g. ~/.vep/homo_sapiens/78_GRCh38/
# or root path (root_dir) e.g. ~/.vep/ where species and version are drawn from config and assembly from config, DB or scanning dir
throw("ERROR: No root_dir or dir specified") unless $hashref && ($hashref->{root_dir} or $hashref->{dir});
my $dir = $hashref->{dir};
throw("ERROR: No root_dir or dir specified") unless $hashref && ($hashref->{root_dir} or $dir);
throw("ERROR: Directory $dir does not exist") if defined $dir && !-d $dir;

$self->{$_} = $hashref->{$_} for keys %$hashref;

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3 changes: 2 additions & 1 deletion modules/Bio/EnsEMBL/VEP/Config.pm
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Expand Up @@ -227,11 +227,12 @@ our @VEP_PARAMS = (

# cache stuff
'database', # must specify this to use DB now
'cache:s', # use cache (optional param treated like --cache-dir)
'cache:s', # use cache (optional param treated like --dir_cache)
'cache_version=i', # specify a different cache version
'show_cache_info', # print cache info and quit
'dir=s', # dir where cache is found (defaults to $HOME/.vep/)
'dir_cache=s', # specific directory for cache
'full_cache_dir=s', # directory to specific cache to use (ignores --dir_cache if set)
'dir_plugins=s', # specific directory for plugins
'offline', # offline mode uses minimal set of modules installed in same dir, no DB connection
'fasta|fa=s', # file or dir containing FASTA files with reference sequence
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