Due to changes in the structure of the production database, since
release 98 the value of analysis.logic_name corresponding to non-coding
RNA can be either 'ncrna' (which is what we used before) or
'ncrna_species_name'. Change the SQL query used to map RFAM IDs to
Ensembl stable IDs so that it can correctly handle species using the
latter syntax, i.e. human, mouse and zebrafish.

Issue: ENSINT-402

[annual copyright updater]. Bugfix: do not touch symbolic links

Version bump to 101

Core db schema patch to support longer assembly names in the mapping_session table.

ens-carlos authored 5 years ago and Tiago Grego committed 5 years ago

Database schema patch to increase the length of the supported assembly names in the mapping_session table.

Revert "Patch to support longer assembly names in the mapping session table."

Patch to support longer assembly names in the mapping session table.

Gitlab CI: enable triggering of dependent builds on Travis

[ENSCORESW-3183][ENSCORESW-3176] Mapper performance improvements

IntervalTree performance: stop sorting already-sorted intervals and avoid checking for blessed references

Remove Try::Tiny dependency

add basic info to readme

Task variation/remove deprecation status

comment out diag statements in tests

Our Perl images are now all based on Debian Buster so there is no longer
a need to try and install Jessie packages.

Seeing as they were to run even in the event of any of the local
test jobs having failed, no real point in waiting until after the local
jobs have completed.

By building our own images with common dependencies already installed,
we can make actual test runs faster and less wasteful. That said, do
keep directives for installing dependencies here in case of some of them
having been updated since the last rebuild of the images.