Ensembl vep singularity

Question

[quentin54520]

Hello all,

I would like to use variant effect prédictor on an hpc cluster. For that i use singularity with the docker image of vep :

singularity pull --name vep.sif docker://ensemblorg/ensembl-vep

But i have a problem to use one plugin because a perl module is missing.

I get this error :

WARNING: Failed to compile plugin Carol: Can't locate Math/CDF.pm in @INC (you may need to install the Math::CDF module) (@INC contains: /shared/home/quentin67100/.vep/Plugins /opt/vep/src/ensembl-vep/modules /opt/vep/src/ensembl-vep /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.26.1 /usr/local/share/perl/5.26.1 /usr/lib/x86_64-linux-gnu/perl5/5.26 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.26 /usr/share/perl/5.26 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /shared/home/quentin67100/.vep/Plugins/Carol.pm line 76. BEGIN failed--compilation aborted at /shared/home/quentin67100/.vep/Plugins/Carol.pm line 76.

I try these 2 command to solve the problems but without succes :

singularity exec vep.sif cpanm Math::CDF

And:

singularity exec vep.sif cpanm --local-lib-contained /shared/home/quentin67100/.vep/Plugins Math::CDF

Any solution ?

[ATpoint]

Can you try to run it as singularity exec --no-home --cleanenv?

[quentin54520]

You mean something like:

srun singularity exec --no-home --cleanenv /shared/projects/gentaumix/Ressources/VEP/vep.sif \
vep \
--everything \

If yes, it didn't work i obtained the same error message

[ATpoint]

Yes, because it looks like it is scanning your local folders for plugins which is probably not what is supposed to happen when running via a container, everything should be inside the container, no?

Ok, then you have to wait until the Ensembl people (who are active here) stumble over this, sorry.

[quentin54520]

Unfortunately ensembl team will do nothing because it's just for a plugin (and not the whoke program) and they choose to not include this type of optional module in order to keep the image size as small as possible..

I will try to use it with conda

Answer 1

[quentin54520]

Great news ! i found the solution, just add export PERL5LIB=$PERL5LIB:$HOME/perl5 in my bashrc and now the INC contain also the directory /shared/home/quentin67100/perl5

[Kiran]

Hi I also pulled SIF image from docker,, Now how do i execute the VEP from singularity ?

[Ben_Ensembl]

Hi Kiran - there is a description of downloading and running VEP with Singularity 3.5+ in the following blog post:

https://www.ensembl.info/2021/05/24/cool-stuff-the-vep-can-do-singularity/