Installing VEP in conda

Question

[michael.flower.14]

I'm trying to use VEP in a conda environment, but it errors anytime I try and run it.

I installed it with

conda install -c bioconda tnsembl-vep

But every time I try and run anything I get this error. It looks like I need to install a Bio::PrimarySeqI module, but I'm not sure how to do that?

Can't locate Bio/PrimarySeqI.pm in @INC (you may need to install the Bio::PrimarySeqI module) (@INC contains: /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-88.9-0/modules /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-88.9-0 /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/lib/site_perl/5.26.2/x86_64-linux-thread-multi /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/lib/site_perl/5.26.2 /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/lib/5.26.2/x86_64-linux-thread-multi /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/lib/5.26.2 .) at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Slice.pm line 75.
BEGIN failed--compilation aborted at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Slice.pm line 75.
Compilation failed in require at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Feature.pm line 84.
BEGIN failed--compilation aborted at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Feature.pm line 84.
Compilation failed in require at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Variation/BaseVariationFeature.pm line 58.
BEGIN failed--compilation aborted at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Variation/BaseVariationFeature.pm line 58.
Compilation failed in require at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Variation/VariationFeature.pm line 97.
BEGIN failed--compilation aborted at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Variation/VariationFeature.pm line 97.
Compilation failed in require at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm line 89.
BEGIN failed--compilation aborted at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Variation/DBSQL/VariationFeatureAdaptor.pm line 89.
Compilation failed in require at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-88.9-0/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 47.
BEGIN failed--compilation aborted at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-88.9-0/modules/Bio/EnsEMBL/VEP/BaseVEP.pm line 47.
Compilation failed in require at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/lib/site_perl/5.26.2/base.pm line 100.
    ...propagated at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/lib/site_perl/5.26.2/base.pm line 109.
BEGIN failed--compilation aborted at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-88.9-0/modules/Bio/EnsEMBL/VEP/BaseRunner.pm line 46.
Compilation failed in require at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/lib/site_perl/5.26.2/base.pm line 100.
    ...propagated at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/lib/site_perl/5.26.2/base.pm line 109.
BEGIN failed--compilation aborted at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/share/ensembl-vep-88.9-0/modules/Bio/EnsEMBL/VEP/Runner.pm line 46.
Compilation failed in require at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/bin/vep line 20.
BEGIN failed--compilation aborted at /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/conda/envs/bioinfo/bin/vep line 20.

[Asaf]

Did the install end up with an error message? Try installing it in a fresh environment. I personally prefer to work with containers (singularity/docker).

[jon.klonowski]

How has this not been solved???