diff --git a/docs/resources/4_APPENDIX_ex11_viral_taxonomy_prediction_via_vContact2.md b/docs/resources/4_APPENDIX_ex11_viral_taxonomy_prediction_via_vContact2.md index b9f5c334..da18f93f 100644 --- a/docs/resources/4_APPENDIX_ex11_viral_taxonomy_prediction_via_vContact2.md +++ b/docs/resources/4_APPENDIX_ex11_viral_taxonomy_prediction_via_vContact2.md @@ -64,16 +64,15 @@ Use `vContact2`'s `vcontact2_gene2genome` script to generate the required mappin # Load modules module purge module unload XALT - module load Singularity/3.11.3 \ + module load Apptainer/1.2.5 \ MCL/14.137-gimkl-2020a \ DIAMOND/2.1.9-GCC-11.3.0 - # Bind path to Singularity container - export SINGULARITY_BIND="$PWD" + # All NeSI Filesystems are pre-bound to APPTAINER_BIND container=/opt/nesi/containers/vContact2 # Run script - singularity run $container/vcontact2.simg \ + apptainer run $container/vcontact2.simg \ vcontact2_gene2genome --proteins viral_taxonomy/checkv_combined.faa \ --output viral_taxonomy/viral_genomes_g2g.csv \ -s 'Prodigal-FAA' @@ -101,16 +100,15 @@ Use `vContact2`'s `vcontact2_gene2genome` script to generate the required mappin # Load modules module purge module unload XALT - module load Singularity/3.11.3 \ + module load Apptainer/1.2.5 \ MCL/14.137-gimkl-2020a \ DIAMOND/2.1.9-GCC-11.3.0 # Bind paths - export SINGULARITY_BIND="$PWD" container=/opt/nesi/containers/vContact2 # Run vConTACT2 - singularity run $container/vcontact2.simg \ + apptainer run $container/vcontact2.simg \ vcontact2 --raw-proteins viral_taxonomy/checkv_combined.faa \ --rel-mode Diamond \ --threads $SLURM_CPUS_PER_TASK \