March 3, 2017

Debian Ensembl update

Eagle's DebianMed contribution of a fully-working .deb file to install Ensembl is almost complete. The demonstration version 57 contains only minor issues now that need to be resolved before it can be released through the Debian package management process.

Those issues are:

  • Removal of the embedded JALView as it breaks a lot of Debian's licensing terms.
  • Removal of the redundant internal copy of Bio::Das::Lite, which is now available on CPAN and is a better version (no longer uses LWP::Parallel::UserAgent).
  • Removal of the LWP::Parallel::UserAgent dependency from one last place where it occurs inside Ensembl. This by default will also remove the dependency on the ancient 5.808 version of libwww-perl and allow it to work with the most recent versions instead.
  • Rewriting blastview code to make it bioperl version-agnostic (this is the sole location where there is still a dependency on bioperl-1.2.3)

As it stands, the current .deb has workarounds that allow all of the above to be skipped, but it is not pretty! So we don't feel we can release it until these issues are fixed. However they're all underway and naturally in the spirit of open-source if anyone has any comments to make or patches to contribute that address the above issues, we'd be happy to hear from you.

Topics: Big data technology, Bioinformatics, Debian, Ensembl, Open source