[ensembl-dev] docker for version 103.1 and problem downloading CHECKSUMS

Andrew Parton aparton at ebi.ac.uk
Thu Feb 18 19:46:01 GMT 2021


Hi Michael,

Thank you for getting in touch. Docker 103.1 should be available now, you can update with `docker pull ensemblorg/ensembl-vep`.

Additionally, the CHECKSUMS issue should also now be resolved. Please let me know if you have any issues when rerunning and I can take a closer look.

Kind Regards,
Andrew

> On 18 Feb 2021, at 19:07, Michael Yourshaw <myourshaw at gmail.com> wrote:
> 
> I get the following message running
> docker run -t -i \
> -v /mnt/hdd/dnanexus/docker/vep_mounted_volumes/GRCh38/vep_data:/opt/vep/.vep \
> ensemblorg/ensembl-vep \
> perl INSTALL.pl -a cfp -s homo_sapiens_merged -y GRCh38 -g all \
> ;
> 
> Version check reports there are post-release updates available of ensembl-vep (installed: 103.0, available: 103.1)
> 
> You should exit this installer and re-download 'ensembl-vep' if you wish to update
> 
> Do you wish to exit so you can get updates (y) or continue (n): n
> 
> How would I get 103.1 via docker?
> 
> Having accepted version 103, after the genome fastq downloads, the INSTALL process fails with
> 
> #- getting list of available cache files
> NB: Remember to use --merged when running the VEP with this cache!
>  - downloading ftp://ftp.ensembl.org/pub/release-103/variation/indexed_vep_cache/homo_sapiens_merged_vep_103_GRCh38.tar.gz <ftp://ftp.ensembl.org/pub/release-103/variation/indexed_vep_cache/homo_sapiens_merged_vep_103_GRCh38.tar.gz>
> Cannot open Local file /opt/vep/.vep/tmp/CHECKSUMS: No such file or directory
>  at INSTALL.pl line 1244.
> curl failed (150), trying to fetch using LWP::Simple
> LWP::Simple failed (404), trying to fetch using HTTP::Tiny
> Use of uninitialized value in numeric eq (==) at /usr/share/perl/5.26/HTTP/Tiny.pm line 606.
> Use of uninitialized value in numeric eq (==) at /usr/share/perl/5.26/HTTP/Tiny.pm line 606.
> ERROR: Failed last resort of using HTTP::Tiny to download ftp://ftp.ensembl.org:21/pub/release-103/variation/indexed_vep_cache/CHECKSUMS <ftp://ftp.ensembl.org/pub/release-103/variation/indexed_vep_cache/CHECKSUMS>
> 
> 
>> Michael Yourshaw
> myourshaw at gmail.com <mailto:myourshaw at ucla.edu>
> 
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