Trouble Running VEP in Conda Environment Due to Perl DBD::mysql Error

Question

[qiuting]

Hello BioStars Community,

I am currently facing issues with running the Variant Effect Predictor (VEP) and vcf2maf in a Conda environment due to a Perl-related error.

Installation Steps: I installed VEP and vcf2maf using Conda with the following commands, and everything installed without any problems:

conda create -n vcf2maf -y python=3.8
conda activate vcf2maf 
conda install -y  -c bioconda vcf2maf 
conda install  -y  -c bioconda ensembl-vep 
conda install  -y   -c bioconda samtools 
vcf2maf.pl  --help 
vep --help  
samtools -v 
perl -e '{print join"\n",@INC}

Cache Installation: I then installed the cache for VEP using these commands:

export VEP_PATH=$HOME/vep 
export VEP_DATA=$HOME/.vep 
mkdir -p $VEP_PATH $VEP_DATA 
cd $VEP_PATH
vep_install -a cf -s homo_sapiens -y GRCh38 -c  $VEP_PATH --CONVERT
#  downloading ftp://ftp.ensembl.org/pub/release-88/variation/VEP/homo_sapiens_vep_88_GRCh38.tar.gz
cd $HOME/.vep nohup wget
ftp://ftp.ensembl.org/pub/release-101/variation/indexed_vep_cache/homo_sapiens_vep_101_GRCh38.tar.gz & 
tar zxvf homo_sapiens_vep_101_GRCh38.tar.gz

Error during Test Run: However, when I tried to test run VEP with the following command:

vep --help
# By default the VEP uses $HOME/.vep/  
vep  -i test_varscan.vcf  -o test.vcf  \
--cache --dir_cache $HOME/vep --force_overwrite  --assembly GRCh38 --vcf

I encountered the following error:

perl: relocation error: /public2/qiuting/.conda/envs/vcf2maf/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi/auto/DBD/mysql/mysql.so:symbol mysql_options4, version libmysqlclient_18 not defined in file libmysqlclient.so.18 with link time reference

Attempts to Resolve: To resolve this, I tried:

cpanm DBD::mysql  
conda install -c conda-forge perl-dbd-mysql

Unfortunately, these attempts did not resolve the issue, and the same error occurred.

I am not very familiar with Perl and its modules. Could anyone please help me solve this issue? Any suggestions or insights would be greatly appreciated!

Thank you in advance!

[qiuting]

i solve it by adding "--offline"

vep  -i test_varscan.vcf  -o test.vcf  \
--cache --dir_cache $HOME/vep --force_overwrite  --assembly GRCh38 --vcf --offline

[colindaven]

I found this page https://www.ensembl.info/2021/05/24/cool-stuff-the-vep-can-do-singularity/ useful some time ago to get VEP working with Singularity without being troubled by perl dependencies.