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### Description of feature
It would be nice to have an example where we directly connect to the ensembl mysql servers to run a query. Especially for the biomart version, much more information should …
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Update the following URL to point to the GitHub repository of
the package you wish to submit to _Bioconductor_
- Repository: https://github.com/js2264/EnsemblGenomes
Confirm the following by ed…
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The [search_phenotype_association_sets](https://github.com/ga4gh/ga4gh-client/blob/master/ga4gh/client/client.py#L749-L758) method (and presumably other methods that use the `ga4gh.client.protocol` m…
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POSTGAP never finishes my run, citing problems with VEP timing out for connection. It seems to be having problems with this SNP (not in the input dataset):
`CRITICAL - Failed to get proper response…
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Hi,
I am having an issue with refgenie pull. This is a fresh install of refgenie on a server running CentOS7. Basically what happens is that if I try to do a refgenie pull, it seems to connect with…
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Hello, i have a problem creating an annotation file for Seurat with GetGrangesFromEnsDb().
While curating the single-cell experiments, a certain [GTF](https://ftp.ensembl.org/pub/release-97/gtf/mus_…
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Hello,
While running FastOMA on 2200 species, I encountered another mafft segmentation fault but when I resumed nextflow it seemed to not complain about the segmentation fault but I got the recursio…
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When I run the following command to import Ensembl databases, it occurs error like this:
Command:
```
docker run --rm \
--name genomehubs-ensembl \
--network genomehubs-…
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Got the SOP from Bruno, following the documentation with help from Peter.
[EnsGen-ProjectingAcrossAssembly2019Apr.pdf](https://github.com/warelab/gramene/files/3167553/EnsGen-ProjectingAcrossAssembly…
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Hello All,
First of all, thank you for implementing the variant recoder tool.
I have a very specific question about speeding up the variant recoder. I have ~21 million variants that I want to qu…