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Merge hg38 branch to master? #84
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Any news about merge? I've simple installed different assemblies in different folders, but this is not very elegant solution and I have to use different directory than for all other VEP plugins. |
@konradjk What about merging this branch from @willmclaren? |
Another hint for the record: VEP_SHARE=$CONDA_PREFIX/share/ensembl-vep-$VERSION
rm $VEP_SHARE/TissueExpression.pm \
$VEP_SHARE/ancestral.pm \
$VEP_SHARE/context.pm \
$VEP_SHARE/de_novo_donor.pl \
$VEP_SHARE/extended_splice.pl \
$VEP_SHARE/gerp_dist.pl \
$VEP_SHARE/loftee_splice_utils.pl \
$VEP_SHARE/splice_site_scan.pl \
$VEP_SHARE/svm.pl \
$VEP_SHARE/utr_splice.pl Afterwards, you can set |
Hi here !
|
@mhebrard I wouldn't use the docker image you refer to - it is >3 years old and to be honest I can't remember why/how it was created! You might get some debug info by adding If someone wants to have a go creating an up-to-date docker image then be my guest. |
@willmclaren, thanks for the hint on
I tried to specify the correct path to Then I copy the content of
Note that the link to Hope that help others |
Dear @konradjk, would it be possible to merge the hg38 with current master s.t. we have one LOFTEE version that works for both hg19 and hg38?
It's currently very hard to install and use LOFTEE for hg38.
For example, I'm constantly failing to get the hg38 branch working because of conflicting LoF.pm from VEP.
Also, I had a very hard time to figure out which files are needed and which options need to be set since e.g.
gerp_bigwig
does not exist on master.I believe that a merged version of LOFTEE would significantly simplify its usage.
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