The current INSTALL.pl script cannot download VEP files using Net::FTP, as the files are now accessible via HTTPS.

[dolittle007]

Describe the issue

The current INSTALL.pl script cannot download VEP files using Net::FTP, as the files are now accessible via HTTPS only.

Additional information

Please fill in the following sections to help us find the source of your issue as quickly as possible.

System

• VEP version: [e.g. 98 or 98.1]
• VEP Cache version: [e.g. 98]
• Perl version: [e.g. 5.26]
• OS: [e.g. MacOS, Ubuntu, CentOS]
• tabix installed ?

Full VEP command line

INSTALL.pl -a cf -s homo_sapiens -y GRCh38 --CONVERT

will report ERROR: Could not connect to FTP host ftp.ensembl.org
Connection timed out.

Full error message

Including the warnings, if available

Data files (if applicable)

They include:

• The input file
• The output file
• The custom file(s)
  You can provide a sample of them

[nakib103]

Hello @dolittle007,

Thanks for your query.

I cannot reproduce the error with Net::FTP.

% INSTALL.pl -a cf -s felis_catus --CONVERT   
Installation on OSX requires that you set up some paths before running this installer.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

PLEASE REMEMBER TO 
1. add /Users/snhossain/ensembl-repos/ensembl-vep/htslib to your DYLD_LIBRARY_PATH environment variable

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 - getting list of available cache files
 - downloading https://ftp.ensembl.org/pub/release-113/variation/indexed_vep_cache/felis_catus_vep_113_Felis_catus_9.0.tar.gz
 - unpacking felis_catus_vep_113_Felis_catus_9.0.tar.gz
 - converting cache, this may take some time but will allow VEP to look up variants and frequency data much faster
 - use CTRL-C to cancel if you do not wish to convert this cache now (you may run convert_cache.pl later)
2025-04-23 10:56:30 - Processing felis_catus
2025-04-23 10:56:30 - Processing version 113_Felis_catus_9.0
2025-04-23 10:56:30 - No unprocessed types remaining, skipping
2025-04-23 10:56:30 - All done!
 - downloading Felis_catus.Felis_catus_9.0.dna.toplevel.fa.gz

All done

Can you double check that FTP port is not blocked from your firewall?

Best regards,
Nakib

[nakib103]

Hi @dolittle007,

With the release of Ensembl VEP 114 you now use HTTPs protocol to install Ensembl VEP cache and FASTA files. Just add the USE_HTTPS_PROTO option in your install command -

INSTALL.pl -a cf -s homo_sapiens -y GRCh38 --CONVERT --USE_HTTPS_PROTO

Best regards,
Nakib

[nakib103]

Hi, I will close this issue. If you face any more problems feel free to reach out.