update singularity pipeline for new ebi cluster

obophenotype · Aug 14, 2023 · 1c69530 · 1c69530
1 parent 7c3ac0f
commit 1c69530
Showing 1 changed file with 16 additions and 3 deletions.
diff --git 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
+
+
+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."
+
+