language suffix: vep.pl vs vep about ensembl-vep HOT 3 CLOSED

OK, agreed, see 3e5ae98

This will appear in release/88 when available, for now only on master.

from ensembl-vep.

When scripts are installed into a directory in the system PATH, the script name should not include an extension such as .sh or .pl that denotes the scripting language currently used to implement it.

We don't suggest users install VEP into system PATH, though there's nothing to stop you doing so if it better suits your pattern of usage.

It's also straightforward to use alias to get the same effect.

from ensembl-vep.

We don't suggest users install VEP into system PATH, though there's nothing to stop you doing so if it better suits your pattern of usage.

Even if not installing system-wide, using it with environment modules or otherwise setting PATH presents the same situation-- it's a user-facing program that exposes implementation details. Running pipelines out of a set of extracted download archives gets messy quickly.

It's also straightforward to use alias to get the same effect.

That's true, but I'd like for us to agree on this-- using the name that you decide improves portability of scripts and workflows based on VEP.

from ensembl-vep.