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Disconnect connection to hive database if not used. This is to avoid … #60

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wants to merge 29 commits into from
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Disconnect connection to hive database if not used. This is to avoid … #60

wants to merge 29 commits into from

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thomasmaurel
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…getting a failed job if it has been running for more than 8h.
This is a problem that we have experienced with Anja when server is under a high load and when running the dump GVF script.

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Coverage Status

Coverage remained the same at 80.787% when pulling 73801c8 on thomasmaurel:registry_and_divisions_support_release_90 into 99ae5d5 on Ensembl:update_release_dumping.

@thomasmaurel
Update SubmitJob.pm
9935d31 
Fixed previous commit to allow this runnable to be run as a standalone.
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Coverage Status

Coverage remained the same at 80.787% when pulling 9935d31 on thomasmaurel:registry_and_divisions_support_release_90 into 99ae5d5 on Ensembl:update_release_dumping.

William McLaren and others added 21 commits July 26, 2017 14:44
fix vcf config paths
8aa865b
add gnomAD to favoured list of pops for max AF
41183cf
add get_matched_variant_alleles util method
19d1f5f
use get_matched_variant_alleles to compare VF to VCF
7d3984b
fix for ref copying bug
b6f722e
@sarahhunt
HGVS fix for long subs
94697a0
create MTMP_transcript_variation table from scratch on init
262ced4
patch test DBs to e90
44453ce
FastaSequence.pm now also overrides Slice::subseq
d896527
reverting d896527 as it is causing REST to fail
bd654fe
reverting d896527 as it is causing REST to fail
74b6e9a
reimplement fixed subseq override in FastaSequence
bd72685
properly map VCF->VF alleles; add code to catch alleles found in VCF …
5f09cd2 
…but not in VF
Fix external link
dd91d79
Actually there is no need to have extra link parameters
7232ef8
Remove the import of the allele data into the 'allele' table for HGMD…
300dd68 
… and COSMIC
Use the vcf_config.json file to get the population list for some proj…
e22dea8 
…ects instead of listing them directly into the script
@at7
only add synonyms if vf has attached variation object
e4f3fb8
@at7
update values
ef37418
@at7
update dump split slice
47e8c78
@at7
compute base before insertion
95add60
Merge branch 'master' of https://github.com/Ensembl/ensembl-variation …
8955df5 
…into registry_and_divisions_support_release_90
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Coverage Status

Coverage increased (+0.2%) to 81.025% when pulling 8955df5 on thomasmaurel:registry_and_divisions_support_release_90 into 99ae5d5 on Ensembl:update_release_dumping.

@thomasmaurel thomasmaurel deleted the registry_and_divisions_support_release_90 branch August 21, 2017 09:25
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@thomasmaurel @coveralls @mkschuster @sarahhunt @at7