[ensembl-dev] Changes to Ensembl Perl version support

[Kieron Taylor]

Dear dev readership,

TL;DR 
- Ensembl would like to stop supporting/testing Perl older than 5.14 in order to extend support to 5.26.
- Specific products, especially the VEP can continue to support older versions
- Ensembl intends to increase the recommended BioPerl version from 1.6.1 to 1.6.924
- The changes should not impact existing installations or archives, but will affect upgrades
- The changes would occur in release 93, currently scheduled for late June 2018 (TBC)
- Contact us if this would have negative impact for you, e.g. you need Perl 5.10

Long version:

Three years have passed since Ensembl last changed the recommended Perl versions. We are now considering this question again, with a view to reducing our need to support older Perl versions and provide better support to much newer versions (5.18 and up). This impacts all components of our Perl APIs, Ensembl REST, website components, and potential installations of BioPerl. VEP will continue to provide support for older Perls to suit specific deployments.

We propose to raise the minimum supported Perl version for the majority of Ensembl components to 5.14.4, with a recommended and tested Perl of 5.26.1.

We have taken steps to ensure that the Ensembl APIs will be Perl agnostic, so that as of release 93 all versions of Perl between 5.14 and 5.26 should work consistently. This encompasses the defaults of various long-term stable Linux distros and Mac OS, who at this time are defaulting to either 5.16 or 5.18, while also providing more support to users running on the latest flavours of Fedora, Ubuntu etc. Older Perl versions should continue to work as before, but we would no longer be able guarantee their continued function if you upgrade your Ensembl installations.

If you have any objections to a minimum Perl of 5.14, please raise them on dev at ensembl.org or address them to helpdesk at ensembl.org so that we can take your needs into account when deciding whether to go ahead with these changes. The same applies to any other concerns you have on this topic.

For those of you with no admin privileges on your computers, we recommend you manage your own Perl software using plenv [1] or Perlbrew [2] to build and switch between Perl versions.

BioPerl version change:

In order to support newer Perl versions, we are forced to require a newer BioPerl version with Ensembl APIs. We are aware of incompatibilities between BioPerl 1.6.1 and Perl versions starting with 5.18 that become showstoppers with 5.22. Additionally we have an issue with the latest BioPerls (1.7.x), but the scope is limited to production of GTF/GFF files. As such the newest BioPerls will also work but a small portion of Ensembl functionality will be incorrect. 1.6.924 is the newest BioPerl release we trust that is compatible with newer Perl versions. It is my hope that this issue will be resolved soon, and we will be able to recommend BioPerl 1.7.2 as well.

Most of our users should not see any issues with BioPerl, but if you run a new Perl version with Ensembl, you will need to change your installed BioPerl to avoid compilation issues.

In summary:

Ensembl needs to move with Perl [3]. We are aware that there are restrictions on our user environments, but hopefully those restrictions evolve with time. Do let us know if anything I have said alarms you, and we will try to accommodate your needs.


Regards,

Kieron

[1] - https://github.com/tokuhirom/plenv
[2] - https://perlbrew.pl/
[3] - No we can't move off Perl at this point in time.


Kieron Taylor PhD.
Ensembl Developer

EMBL, European Bioinformatics Institute