This project is mirrored from https://:*****@github.com/Ensembl/ensembl.git.
Pull mirroring updated .
- 19 Jun, 2019 1 commit
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Marek Szuba authored
Test DBs: fix broken application of the Compara schema-version bump
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- 18 Jun, 2019 3 commits
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Marek Szuba authored
The last time we ran patch_test_databases for release 98 it somehow managed to apply compara's patch_97_98_b without applying patch_97_98_a. I don't even.
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Marek Szuba authored
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Marek Szuba authored
Release-98 version bump
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- 17 Jun, 2019 7 commits
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Marek Szuba authored
Source: release/98 branch of ols-ensembl-loader and master branches of all other relevant Ensembl repositories, pulled a few minutes ago. Compara, Variation and ontology schemas all have already been bumped to version 98.
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Marek Szuba authored
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Marek Szuba authored
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Marek Szuba authored
The ontology schema patches have been moved from ensembl/misc_scripts…
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Marek Szuba authored
ENSCORESW-3132: Limited implementation of Intervals with start > end …
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Thomas Maurel authored
The ontology schema patches have been moved from ensembl/misc_scripts/ontology/sql to ols-ensembl-loader/sql
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Brandon Walts authored
ENSCORESW-3132: Limited implementation of Intervals with start > end (i.e. spanning the origin of a circular chromosome)
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- 14 Jun, 2019 2 commits
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Marek Szuba authored
Remove deprecated GOTermAdaptor and SOTermAdaptor modules
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Marek Szuba authored
Travis: Add mysql to the list of services [master]
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- 13 Jun, 2019 1 commit
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Marek Szuba authored
Enable VGNC xrefs for felis_catus, macaca_mulatta and microcebus_murinus
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- 11 Jun, 2019 1 commit
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Marek Szuba authored
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- 07 Jun, 2019 1 commit
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Marek Szuba authored
Deprecated since 2011, non-functional since March 2018. See ENSCORESW-2871. Note that there is still a reference to GOTermAdaptor in the xref parser GOSlimParser. However, the parser in question seems to be no longer used and in any case has not been updated, other than changing the copyright notices, for years.
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- 24 May, 2019 2 commits
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Marek Szuba authored
Ubuntu Xenial, which is now being rolled out as the default Linux distro for Travis builds following the end of life of Ubuntu Trusty, does not start services such as MySQL unless told to. We use the default distro in our builds so we are likely to be affected.
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Marek Szuba authored
Make the Coveralls badge in the README work
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- 15 May, 2019 1 commit
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Tiago Grego authored
ENSCORESW-3147: correctly capture all required fields from file
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- 14 May, 2019 3 commits
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Magali Ruffier authored
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Marek Szuba authored
The new Coveralls URI points to SVG so let us stick with a single format for all badges.
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Marek Szuba authored
The Coveralls URI need to contain the branch name for the badge to work, moreover URIs for GitHub repositories are (now?) different. The URIs use now both are what Coveralls Web site suggests and have been demonstrated to work in case of ensembl-xref.
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- 08 May, 2019 3 commits
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ens-bwalts authored
Registry: add support for versioned ensembl_metadata DBs [master]
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Marek Szuba authored
appris method on Transcript
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Marek Szuba authored
See ENSCORESW-3119. If both a versioned and an unversioned database are present, use the versioned one if the version number matches that of the software.
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- 03 May, 2019 1 commit
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Tiago Grego authored
Store web_data without newlines
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- 02 May, 2019 1 commit
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James Allen authored
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- 29 Apr, 2019 3 commits
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Tiago Grego authored
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Tiago Grego authored
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Tiago Grego authored
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- 26 Apr, 2019 2 commits
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Marek Szuba authored
Changed attribute code length to 14 characters.
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Shamika Mohanan authored
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- 25 Apr, 2019 3 commits
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Kieron Taylor authored
Add support for stop codon readthrough as a type of edit.
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Shamika Mohanan authored
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Shamika Mohanan authored
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- 17 Apr, 2019 4 commits
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Shamika Mohanan authored
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Shamika Mohanan authored
Code updated to implement review comments. There is a new package to handle stop codon readthrough in a sequence. Test case has been updated with new regex
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Marek Szuba authored
The previous test-database update missed some patches for the core and variation schemas, which is why Travis jobs keep failing these days.
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Shamika Mohanan authored
ENSCORESW-3110- Code to handle stop codon readthrough in 12 transcripts. The code edits the amino acid sequence to display the stop codon readthrough with an X
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- 15 Apr, 2019 1 commit
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ens-bwalts authored
[ENSCORESW-3077] Travis: Unify configuration of Slack notifications
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