"Input file does not exist" error message when using the Windows version of ensembl-vep with Docker‏‏‏‏

Question

[langziv]

Hello.

I installed and run vep in Windows with Docker. The API version I installed is 104. I first started vep with the command

"docker run -t -i -v $HOME/vep_data:/opt/vep/.vep ensemblorg/ensembl-vep"

,then run the program with an input file with the command

"./vep --database -i C:/Users/97254/PycharmProjects/weizmann/ outputs/opn1lw_variants.txt -o ."

,which yielded the following error message:

-------------------- EXCEPTION --------------------
MSG: ERROR: File "C:/Users/97254/PycharmProjects/weizmann/outputs/opn1lw_variants.txt" does not exist

STACK Bio::EnsEMBL::VEP::Parser::file /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser.pm:231
STACK Bio::EnsEMBL::VEP::Parser::new /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Parser.pm:125
STACK Bio::EnsEMBL::VEP::Runner::get_Parser /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:801
STACK Bio::EnsEMBL::VEP::Runner::get_InputBuffer /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:828
STACK Bio::EnsEMBL::VEP::Runner::init /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:136
STACK Bio::EnsEMBL::VEP::Runner::run /opt/vep/src/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:199
STACK toplevel ./vep:232
Date (localtime)    = Mon Nov 22 07:51:51 2021
Ensembl API version = 104
---------------------------------------------------

I'd love to get some ideas regarding what I did wrong. Thanks.

[cpad0112]

Make sure that you have ENSEMBL suggested docker setup for easy troubleshooting esp input, in this case.

Answer 1

[Michal @Ensembl]

Hi. We have a blog post on installing VEP on windows 10 here: https://www.ensembl.info/2021/08/09/cool-stuff-the-vep-can-do-installation-on-windows-10/ What was the installation command you used?

[langziv]

It works (finally)!

[Michal @Ensembl]

That's brilliant. I'm glad it works now.

Answer 2

[Emily]

Have you correctly mounted the folder containing your input file to Docker? The instructions here explain how to mount a drive.

[langziv]

I'm not sure. Do I need to install gcc, g++ and make for running vep on windows?

I followed the instructions up to Cache and Plugins installation, in which it's explained that the user will be prompted by the installer. I wasn't prompted so I'm not sure if it's installed correctly.

[langziv]

I tried installing the Windows version vep again. Now when running the command docker run -t -i -v $HOME/vep_data:/opt/vep/.vep ensemblorg/ensembl-vep I'm getting the documentation output that one gets when using the command --help. Unlike in the first try, now I'm not getting connected to a container.