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- Mar 18, 2020
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Matthieu Muffato authored
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- Mar 17, 2020
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Ameya Chaubal authored
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Ameya Chaubal authored
patch test dbs for 101
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Ameya Chaubal authored
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- Feb 07, 2020
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ens-bwalts authored
Merge the output of the 2018 xref sprint
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- Feb 06, 2020
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Magali Ruffier authored
patch for BaseParser.pm
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- Jan 27, 2020
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ens-bwalts authored
Enable VGNC xrefs for 15 more species
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- Jan 24, 2020
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Marek Szuba authored
cebus_capucinus_imitator 1737458 saimiri_boliviensis_boliviensis 39432 Committing these two separately from the other 12 on the off chance three-part names could cause problems - especially in case of Capuchin, which appears as 'Cebus capucinus imitator' on the Ensembl species list but whose database prefix is simply 'cebus_capucinus'.
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Marek Szuba authored
aotus_nancymaae 37293 carlito_syrichta 1868482 cercocebus_atys 9531 chlorocebus_sabaeus 60711 macaca_fascicularis 9541 macaca_nemestrina 9545 mandrillus_leucophaeus 9568 nomascus_leucogenys 61853 otolemur_garnettii 30611 pan_paniscus 9597 propithecus_coquereli 379532 rhinopithecus_bieti 61621
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Marek Szuba authored
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Tiago Grego authored
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- Jan 20, 2020
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Marek Szuba authored
Yearly copyright update [feature/xref_sprint]
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- Jan 17, 2020
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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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Tiago Grego authored
Yearly copyright update
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Tiago Grego authored
[ENSCORESW-3368] update HGNC data field
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- Jan 16, 2020
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Tiago Grego authored
JSON-formatted web_data
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- Jan 14, 2020
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Tiago Grego authored
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- Jan 10, 2020
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James Allen authored
Changes to test and test dbs to account for web_data being a string rather than a flattened hash that needs special treatment.
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James Allen authored
The web_data field is no longer a flattened Perl hash (hooray\!), it's JSON-formatted. So no longer need the evals, can just treat it as a string. Attendant webcode changes have also been made, and are ready to be tested.
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- Jan 09, 2020
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Tiago Grego authored
RFAMParser: relax selection criteria on analysis.logic_name
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- Jan 08, 2020
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Marek Szuba authored
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
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Tiago Grego authored
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- Jan 07, 2020
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Tiago Grego authored
[annual copyright updater]. Bugfix: do not touch symbolic links
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- Jan 02, 2020
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Tiago Grego authored
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Matthieu Muffato authored
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- Dec 24, 2019
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Tiago Grego authored
Version bump to 101
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- Dec 20, 2019
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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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Tiago Grego authored
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- Dec 19, 2019
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Marek Szuba authored
While at it, fix inconsistent indendation of the licence-and-copyright block in some of the test-suite files.
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- Dec 18, 2019
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Marek Szuba authored
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Marek Szuba authored
To begin with, uncomment both features. I do not think I even want to know what the logic behind having this commented out in the first place was. It must have happened before Ensembl got migrated to GitHub though, judging from commit history. Secondly, update the list of dependencies of the xref_mapping feature so that it reflects what is really needed (read: mostly add missing ones). Finally, get rid of misc-scripts/xref_mapping/cpanfile .
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Marek Szuba authored
The feature 'xref_mapping' is needed by the xref test suite and given how few additional dependencies 'assembly_mapping' adds, let's just enable *all* features to keep things simple.
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Marek Szuba authored
These are used by the xref test suite. We do not presently run these tests on SQLite but let's have that configured as well, just in case.
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Marek Szuba authored
Do not run it in SQLite mode because XrefParser::BaseParser features several occurences of "INSERT IGNORE", which SQLite does not understand. Not that we _need_ SQLite support in the xref pipeline at this point.
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Marek Szuba authored
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Marek Szuba authored
getline_hr() creates a new hashref for every row so even Text::CSV authors themselves recommend using a combination of bind_columns() with getline() instead.
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