Workaround for CARD database download

[DiegoBrambilla]

Hi MEG team,

I see from main_AmrPlusPlus_v2_withRGI.nf that the download of the CARD database fails.

I have managed to download and compress the CARD database for RGI through command line by adding the flag --no-check-certificate

$ wget --no-check-certificate -q -O card-data.tar.bz2 https://card.mcmaster.ca/latest/data && tar xfvj card-data.tar.bz2

This is necessary because the host websie of CARD has an expired certificate:

$ wget https://card.mcmaster.ca/latest/data
--2020-06-03 10:24:44--  https://card.mcmaster.ca/latest/data
Resolving card.mcmaster.ca (card.mcmaster.ca)... 130.113.77.126
Connecting to card.mcmaster.ca (card.mcmaster.ca)|130.113.77.126|:443... connected.
ERROR: cannot verify card.mcmaster.ca's certificate, issued by ‘/C=GB/ST=Greater Manchester/L=Salford/O=Sectigo Limited/CN=Sectigo RSA Organization Validation Secure Server CA’:
  Issued certificate has expired.
To connect to card.mcmaster.ca insecurely, use `--no-check-certificate'.

I attach here a file with the command line I have used.

Please tell me if it helps. Best Brambilla Diego download_CARD.txt

[meglab-metagenomics]

Hi Diego,

This is quite interesting because I just tried the same command wget command without the "--no-check-certificate" flag and the database downloaded just fine for me. Do you think your error could be associated with your VPN or connection to CARD's server (Canada) from Italy?

Either way, I added your suggestion to our README.md file in case other people run into the same issue. I'll close this issue for now, but let me know if you run into any further issues.

Thank you so much for your input! You are helping us make AMR++ better and we appreciate it. Best, Enrique and MEG