amrfinder_update cannot connect to FTP and thus download #bug #help #120
Description
Hello,
I'm struggling installing AMRFinder in my institution. It keeps failing because it cannot find the ftp site:
amrfinder_update --database /home/bioinf/bioinf_archive/98_mökiDatabases/bakta/db/amrfinderplus-db
Running: amrfinder_update --database /home/bioinf/bioinf_archive/98_mökiDatabases/bakta/db/amrfinderplus-db
Looking up the published databases at https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/
*** ERROR ***
CURL: Cannot read from https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/
HOSTNAME: ?
SHELL: /bin/bash
PWD: /home/bioinf
PATH: /home/bioinf/mambaforge/envs/bakta/bin:/home/bioinf/mambaforge/condabin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin
Progam name: amrfinder_update
Command line: amrfinder_update --database /home/bioinf/bioinf_archive/98_mökiDatabases/bakta/db/amrfinderplus-db
but curl is working fine:
curl https://ftp.ncbi.nlm.nih.gov/pathogen/Antimicrobial_resistance/AMRFinderPlus/database/
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 3.2 Final//EN">
<html>
<head>
<title>Index of /pathogen/Antimicrobial_resistance/AMRFinderPlus/database</title>
</head>
<body>
<h1>Index of /pathogen/Antimicrobial_resistance/AMRFinderPlus/database</h1>
<pre>Name Last modified Size <hr><a href="/pathogen/Antimicrobial_resistance/AMRFinderPlus/">Parent Directory</a> -
<a href="3.10/">3.10/</a> 2021-12-22 13:07 -
<a href="3.2/">3.2/</a> 2019-10-31 11:24 -
<a href="3.6/">3.6/</a> 2020-03-25 08:36 -
<a href="3.8/">3.8/</a> 2020-10-02 15:43 -
<a href="3.9/">3.9/</a> 2020-12-21 10:09 -
<a href="3.10/">3.10/</a> 2022-10-12 10:00 -
<a href="3.11/">3.11/</a> 2022-10-12 10:00 -
<a href="latest/">latest/</a> 2021-12-22 13:19 -
<hr></pre>
So two questions:
-
Is there any way to separate database installation from download?
-
I downloaded and indexed the databases manually, but when I run 'amrfinder' it cannot find the path of the databases by default. Since I am working with a wrapper that I cannot edit, and the binaries in AMRFinder are uneditable, is there any way to change the default path where amrfinder looks for the database?
Thanks.