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

João Eiras joao.eiras at gmail.com
Fri Dec 8 11:44:07 GMT 2017


The VEP INSTALL.pl script, among the many dependencies that it pulls,
pulls the Bio-HTS library.


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


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


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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