Installing ensemble VEP by running INSTALL.pl takes too long.

Question

[lsy9]

How long does it usually take to install Ensembl VEP with INSTALL.pl? I am running INSTALL.pl and I think it's taking too long.

I am trying to install Ensembl VEP with this code:

git clone https://github.com/Ensembl/ensembl-vep.git
cd ensembl-vep
perl INSTALL.pl

This is what I get:

- getting list of available cache files
- downloading https://ftp.ensembl.org/pub/release110/variation/indexed_vep_cache/homo_sapiens_vep_110_GRCh38.tar.gz

I'm not getting any additional information for more than a day. Does it usually take that long to install Ensembl VEP?

[ATpoint]

When I type https://ftp.ensembl.org/pub/release110/variation/indexed_vep_cache/homo_sapiens_vep_110_GRCh38.tar.gz into the browser I get a 404 not found. Guess it is stuck there. I would open an issue at github.

Unrelated, but be sure to use correct tags. It's Ensembl, without trailing "e", so Ensembl folks who are active here actually see your post.

[Ben_Ensembl]

Hi Isy9,

The correct URL has a '-' in the release number (i.e https://ftp.ensembl.org/pub/release-110/variation/indexed_vep_cache/...)

We're not sure why this is happening when you run the INSTALL.pl script as the code has a '-' in the URL. We are looking into this and will let you know where the issue is coming from.

[Ben_Ensembl]

Hi Isy9,

We're not sure why this is happening when you run the INSTALL.pl script as the code has a '-' in the URL.

Can you provide any further information about the steps you took in the installation? Did you run the install using the -CACHE_URL option?

[lsy9]

Thanks for the comment. I've corrected the tag.

Answer 1

[colindaven]

I had better results using their singularity container, though it still wasn't trivial. https://www.ensembl.info/2021/05/24/cool-stuff-the-vep-can-do-singularity/

Also, check your proxy server is set up correctly if you are behind one.

[Ram]

Their singularity container does not seem to contain the cache (which is sensible), so that approach would not solve OP's problem.