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Fixing --get-genomes by adding fallback to https in case http download failed #85

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Fixing --get-genomes by adding fallback to https in case http download failed #85

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7 changes: 6 additions & 1 deletion fastq_screen
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Original file line number Diff line number Diff line change
Expand Up @@ -2467,7 +2467,12 @@ sub get_genomes{
#to a permanent location on the webserver, when more space is made available.
my $location_file = 'www.bioinformatics.babraham.ac.uk/projects/fastq_screen/genome_locations.txt';
my $command = "wget --no-check-certificate $location_file";
!system($command) or die "Could not run command '$command'\n";
if(system($command)) {
warn "HTTP download failed, retrying with HTTPS...\n";
$location_file = 'https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/genome_locations.txt';
$command = "wget --no-check-certificate $location_file";
!system($command) or die "Could not run command '$command'\n";
}
$location_file = 'genome_locations.txt';
open(LOCATION, '<', $location_file) or die "Could not open '$location_file' : $!";
scalar <LOCATION> if $bisulfite; #Use second line in file if --bisulfite mode
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