diff --git a/src/scripts/upheno_pipeline_singularity.sh b/src/scripts/upheno_pipeline_singularity.sh index 7d8654d0..0ea41ba9 100644 --- a/src/scripts/upheno_pipeline_singularity.sh +++ b/src/scripts/upheno_pipeline_singularity.sh @@ -1,9 +1,22 @@ #!/usr/bin/env bash set -e -data=/nfs/production3/spot/sw/dev/monarch/data/upheno-dev/src/scripts +data=/nfs/production/parkinso/spot/upheno2/src/scripts cd $data #singularity pull docker://obolibrary/odkfull -singularity exec --pwd $data docker://obolibrary/odkfull python3 upheno_prepare.py ../curation/upheno-config.yaml -singularity exec --pwd $data docker://obolibrary/odkfull python3 upheno_create_profiles.py ../curation/upheno-config.yaml \ No newline at end of file + + +singularity exec --pwd $data docker://obolibrary/odkfull:v1.3.1 python3 upheno_prepare.py ../curation/upheno-config.yaml +singularity exec --pwd $data docker://obolibrary/odkfull:v1.3.1 python3 upheno_create_profiles.py ../curation/upheno-config.yaml + +singularity exec --pwd $data docker://obolibrary/odkfull:v1.3.1 python3 upheno-stats.py ../curation/upheno-config.yaml + +cd ../ontology/ + +echo Running command from $(pwd) +singularity exec docker://obolibrary/odkfull:v1.4.1 make o sim reports + +echo "Release successfully completed, ready to deploy." + +