[ensembl-dev] VEP INSTALL.pl is not very forward compatible

Pieter Neerincx pieter.neerincx at gmail.com
Fri Dec 8 12:13:39 GMT 2017

Hi all,

I support João's request below. Here @ UMCG we just ran into the same issue this week, when we had to re-deploy software one of our clusters after major maintenance. Once we have performed validation experiments for a specific version we need to be able to re-install exactly that validated version; With the current INSTALL.pl script that is not possible without quite a bit of hacking :o...



> On 8 Dec 2017, at 12:44, João Eiras <joao.eiras at gmail.com> wrote:
> Hi.
> The VEP INSTALL.pl script, among the many dependencies that it pulls,
> pulls the Bio-HTS library.
> https://github.com/Ensembl/ensembl-vep/blob/release/90/INSTALL.pl#L809
> But it always pull the master branch. This means that if I download an
> old release of VEP, like version 85, and try to run that script today,
> it is broken because when release 85 was published, the Bio-HTS
> library had a different folder structure.
> Meanwhile, a fix for that difference in the folders was committed
> https://github.com/Ensembl/ensembl-tools/commit/066fa73a08529e917ac5f0979e2bd7df016a2f31#diff-51f0ea2952ae8378025549cdc377ecb6
> I seriously suggest you amend $biodbhts_zip_github_url to point to the
> version of Bio-HTS which was tested and verified compatible with the
> given VEP release, just like you did with samtools/htslib
> https://github.com/Ensembl/ensembl-tools/commit/a992bb0e31ba7bfe17d0e9abeefa87d89e60910f#diff-51f0ea2952ae8378025549cdc377ecb6
> A more reliable and safe way to do this would be to put two variables
> at the top of the script where $API_VERSION is defined, for instance,
> one variable for each library, with the branch/tag name that should be
> checked out and it compatible with that VEP release.
> For instance, I have an old VEP 87 instance, and the version of biohts
> compatible is 2.9.
> Then, as part of the development process you'd bump and test newer
> versions of these libraries.
> Thank you for your time.
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