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comparison VCF_to_VariantDB.pl @ 9:3b27cae9b359 draft

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New Version. VariantDB checks for Genome Build matching using the Galaxy dbkey variable.
author geert-vandeweyer
date Mon, 14 Jul 2014 03:24:28 -0400
parents db44ff975de8
children
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8:db44ff975de8 9:3b27cae9b359
18 # c = encoded id of bam file (optional) 18 # c = encoded id of bam file (optional)
19 # C = encoded id of Bam index , needed if b is specified => NOT POSSIBLE YET, NEEDS INDEXING ON VARIANTDB SERVER ! 19 # C = encoded id of Bam index , needed if b is specified => NOT POSSIBLE YET, NEEDS INDEXING ON VARIANTDB SERVER !
20 # S = (S)erver addrress to send data to. 20 # S = (S)erver addrress to send data to.
21 # R = (r)oot of galaxy web server (/home/galaxyuser/galaxy-dist) 21 # R = (r)oot of galaxy web server (/home/galaxyuser/galaxy-dist)
22 # H = (H)ost of the galaxy web server (http://my.galaxy.server/galaxy/) 22 # H = (H)ost of the galaxy web server (http://my.galaxy.server/galaxy/)
23 # G = Genome build (dbkey)
23 # F = (F)ormat of input file 24 # F = (F)ormat of input file
24 getopts('v:u:n:a:g:o:b:B:V:c:S:R:H:F:', \%opts); # option are in %opts 25 getopts('v:u:n:a:g:o:b:B:V:c:S:R:H:G:F:', \%opts); # option are in %opts
25
26 $|++; 26 $|++;
27 ################# 27 #################
28 ## CHECK INPUT ## 28 ## CHECK INPUT ##
29 ################# 29 #################
30 if (!exists($opts{'v'})) { 30 if (!exists($opts{'v'})) {
73 73
74 ################## 74 ##################
75 ## TEST USER ID ## 75 ## TEST USER ID ##
76 ################## 76 ##################
77 $email = $opts{'u'}; 77 $email = $opts{'u'};
78 my $response = $conn->post( $url, {'CheckUser' => $email} ); 78 $dbkey = $opts{'G'};
79 my $response = $conn->post( $url, {'CheckUser' => $email,'dbkey' => $dbkey} );
79 my $content = $response->decoded_content(); 80 my $content = $response->decoded_content();
80 81
81 if ($content eq 'OK') { 82 if ($content eq 'OK') {
82 print OUT "Testing User-existence : OK.\n"; 83 print OUT "Testing User-existence and Genome Build: OK.\n";
83 } 84 }
84 else { 85 else {
85 die("ERROR: $content"); 86 die("ERROR: $content");
86 } 87 }
87 88