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nf-core

Hi guys. It seems that the VEP-image, which <https://github.com/nf-core/sarek/blob/20f41d1ce8b7ba296ee22adc71fe2da2ebcae93f/modules/nf-core/ensemblvep/vep/main.nf#L8|Sarek> is using, does have the ensembl-xs optimization installed.

```docker run -it <http://community.wave.seqera.io/library/ensembl-vep:115.2--90ec797ecb088e9a|community.wave.seqera.io/library/ensembl-vep:115.2--90ec797ecb088e9a>
(base) root@8df303d9b8ee:/tmp# perl -MBio::EnsEMBL::XS -e 'print "Ensembl::XS OK, version=${Bio::EnsEMBL::XS::VERSION}\n"'
Can't locate Bio/EnsEMBL/XS.pm in @INC (you may need to install the Bio::EnsEMBL::XS module) (@INC contains: /opt/conda/lib/perl5/5.32/site_perl /opt/conda/lib/perl5/site_perl /opt/conda/lib/perl5/5.32/vendor_perl /opt/conda/lib/perl5/vendor_perl /opt/conda/lib/perl5/5.32/core_perl /opt/conda/lib/perl5/core_perl .).
BEGIN failed--compilation aborted.```
You reckon it was a deliberate choice to leave out that optimization?

The ensembl-xs optimization does seem to be installed in the <https://hub.docker.com/layers/ensemblorg/ensembl-vep/release_111.0/images/sha256-87c92b7128ba20ff6ef9f710987091365b26fde962e2bbf92e7d9408eec6dfa7|official> VEP docker-image from ensembl:

```vep@3f3a15b6c2bc:~$ perl -MBio::EnsEMBL::XS -e 'print "Ensembl::XS OK, version=${Bio::EnsEMBL::XS::VERSION}\n"'
Ensembl::XS OK, version=2.3.2
vep@3f3a15b6c2bc:~$```

mmm, that’s weird. I thought the conda package included the xs module, so the container should also

Thanks ffor the prompt reply, Matthias. It could also just be that I'm not checking it properly.  Il'll try the conda version

So I did

```micromamba create -n vep ensembl-vep=115.2 -c bioconda```
Activated the env, ran

```$ vep
#----------------------------------#
# ENSEMBL VARIANT EFFECT PREDICTOR #
#----------------------------------#

Versions:
  ensembl              : 115.266b84d```
```$ which perl
/home/ubuntu/micromamba/envs/vep/bin/perl```
but still I get

```$ perl -MBio::EnsEMBL::XS -e 'print "Ensembl::XS OK, version=${Bio::EnsEMBL::XS::VERSION}\n"'
Can't locate Bio/EnsEMBL/XS.pm in @INC (you may need to install the Bio::EnsEMBL::XS module) (@INC contains: /home/ubuntu/micromamba/envs/vep/lib/perl5/5.32/site_perl /home/ubuntu/micromamba/envs/vep/lib/perl5/site_perl /home/ubuntu/micromamba/envs/vep/lib/perl5/5.32/vendor_perl /home/ubuntu/micromamba/envs/vep/lib/perl5/vendor_perl /home/ubuntu/micromamba/envs/vep/lib/perl5/5.32/core_perl /home/ubuntu/micromamba/envs/vep/lib/perl5/core_perl .).
BEGIN failed--compilation aborted.```

<@U039DEJ1RJS>: I see you’ve been working on the bioconda-recipe for VEP :slightly_smiling_face:

~I noticed that, in the <https://github.com/bioconda/bioconda-recipes/blob/c02af086088e44414bc17f76c388c7579526b2ff/recipes/ensembl-vep/build.sh#L33C42-L33C52|recipe>, `vep_install` is being run with the option `--NO_BIOPERL` . Could that be related to the fact that the xs-module is missing?~

I’ll try to run some tests to see if it is faster to run VEP from the <https://hub.docker.com/layers/ensemblorg/ensembl-vep/release_111.0/images/sha256-87c92b7128ba20ff6ef9f710987091365b26fde962e2bbf92e7d9408eec6dfa7|official> docker-image which contains the xs-module.