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Use VEP docker #46

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Char-Al opened this issue Jun 27, 2023 · 3 comments
Open

Use VEP docker #46

Char-Al opened this issue Jun 27, 2023 · 3 comments
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Back-end enhancement New feature or request

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@Char-Al
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Char-Al commented Jun 27, 2023

It seems a good idea to use VEP docker image.

see : https://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#docker

@Char-Al Char-Al added enhancement New feature or request Back-end labels Jun 27, 2023
@kyauy
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kyauy commented Jun 29, 2023

could be very nice, currently have hard time to install VEP...

@ardoli
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ardoli commented Jul 11, 2023

singularity container is now installed and tested on the cluster.

@ardoli
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ardoli commented Jul 12, 2023

may be have 2 installations:

  • one singularity container for seal's server, for instant annotation.
    --> need to update the way to launch vep in seal
  • the singularity container one the cluster, for asynchronous, and may be bulk, annotations.
    --> 1 - use only VEP annotated VCFs
    --> 2 - use a directory to put unannotated VCFs, and wait for get VEP annotated VCFs complete files generated by a cron job on cluster.

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