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!
i solve it by adding "--offline"
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.