comparison VCF_to_VariantDB.pl @ 9:3b27cae9b359 draft

New Version. VariantDB checks for Genome Build matching using the Galaxy dbkey variable.

8:db44ff975de8

# c = encoded id of bam file (optional)
# C = encoded id of Bam index , needed if b is specified => NOT POSSIBLE YET, NEEDS INDEXING ON VARIANTDB SERVER !
# S = (S)erver addrress to send data to.
# R = (r)oot of galaxy web server (/home/galaxyuser/galaxy-dist)
# H = (H)ost of the galaxy web server (http://my.galaxy.server/galaxy/)
# F = (F)ormat of input file 
getopts('v:u:n:a:g:o:b:B:V:c:S:R:H:F:', \%opts);  # option are in %opts

$|++;
#################
## CHECK INPUT ##
#################
if (!exists($opts{'v'})) {

##################
## TEST USER ID ##
##################
$email = $opts{'u'};
my $response = $conn->post( $url, {'CheckUser' => $email} );
my $content = $response->decoded_content();

if ($content eq 'OK') {
	print OUT "Testing User-existence : OK.\n";
}
else {
	die("ERROR: $content");
}

9:3b27cae9b359

# c = encoded id of bam file (optional)
# C = encoded id of Bam index , needed if b is specified => NOT POSSIBLE YET, NEEDS INDEXING ON VARIANTDB SERVER !
# S = (S)erver addrress to send data to.
# R = (r)oot of galaxy web server (/home/galaxyuser/galaxy-dist)
# H = (H)ost of the galaxy web server (http://my.galaxy.server/galaxy/)
# G = Genome build (dbkey)
# F = (F)ormat of input file 
getopts('v:u:n:a:g:o:b:B:V:c:S:R:H:G:F:', \%opts);  # option are in %opts
$|++;
#################
## CHECK INPUT ##
#################
if (!exists($opts{'v'})) {

##################
## TEST USER ID ##
##################
$email = $opts{'u'};
$dbkey = $opts{'G'};
my $response = $conn->post( $url, {'CheckUser' => $email,'dbkey' => $dbkey} );
my $content = $response->decoded_content();

if ($content eq 'OK') {
	print OUT "Testing User-existence and Genome Build: OK.\n";
}
else {
	die("ERROR: $content");
}