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Published 20 hours ago • verified publisher icon sanger-pathogens

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Open bgold04 opened this issue 7 years ago • 2 comments

MacMini:bin bgold$ ls -l total 48 -rwxr-xr-x 1 bgold staff 2413 Jan 12 01:19 download_fasta_database -rwxr-xr-x 1 bgold staff 1910 Jan 12 01:19 download_mlst_databases -rwxr-xr-x 1 bgold staff 4584 Jan 12 01:19 get_emm_sequence_type -rwxr-xr-x 1 bgold staff 6542 Jan 12 01:19 get_sequence_type MacMini:bin bgold$ chmod 777 download_mlst_databases MacMini:bin bgold$ ./download_mlst_databases Could not connect to https://pubmlst.org/data/dbases.xml

NB: pasting URL into browser DOES connect and show: This XML file does not appear to have any style information associated with it. The document tree is shown below. Achromobacter spp. https://pubmlst.org/achromobacter 2018-04-11

bgold04 avatar Apr 11 '18 17:04 bgold04

If your behind a proxy you may have to set the HTTPS_PROXY environment variable for it to work on the command line. To be honest @tseemann has better software to address the same problem https://github.com/tseemann/mlst

I also have a review paper comparing different MLST methods if that helps: http://mgen.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.000124

andrewjpage avatar Apr 11 '18 18:04 andrewjpage

Hi, I have the same issue : Could not connect to https://pubmlst.org/data/dbases.xml My HTTPS_PROXY environment variable is well defined Do you have any solution ? Best, Fabien

fabgenomics avatar Nov 05 '20 10:11 fabgenomics