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

[qiuting Zhang]

Hello SEQanswers 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..._GRCh38.tar.gz
cd $HOME/.vep nohup wget
ftp://ftp.ensembl.org/pub/release-10..._GRCh38.tar.gz &
tar zxvf homo_sapiens_vep_101_GRCh38.tar.gz
```
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
```
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!

[jgreenbaum]

For the sake of running a quick test, I followed the steps you outlined in the condaforge/mambaforge Docker container with a small genome reference and I was not able to reproduce the issue. I noticed though that the conda environment that is created doesn't seem to have the mysqlclient libraries installed. I wonder if the issue is that the DBD::mysql library is using a system libmysqlclient.so rather than something inside the conda environment? Maybe try

conda install mysqliclient