Merge pull request #35 from ScilifelabDataCentre/FREYA-847/Abdullah-C…

…linMicro update 10 minutes runner for clicmicro visualization
ScilifelabDataCentre · Oct 4, 2024 · 599a496 · 599a496
2 parents a7f41d5 + 2d74667
commit 599a496
Showing 1 changed file with 4 additions and 0 deletions.
diff --git a/runner_every10mins.sh b/runner_every10mins.sh
@@ -14,6 +14,10 @@ PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/wastewater python "$CODE
 PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/serology python "$CODE_PATH"/pathogens-portal-visualisations/serology/weekly-serology-tests.py > "$CODE_PATH"/output/weekly_serology_tests.json
 PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/serology python "$CODE_PATH"/pathogens-portal-visualisations/serology/cumulative-serology-tests.py > "$CODE_PATH"/output/cumulative_serology_tests.json
 
+# ClinMicro statistics is based on these files under /pathogens-portal-visualisations/ClinMicro:
+PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/ClinMicro python "$CODE_PATH"/pathogens-portal-visualisations/ClinMicro/lineage-plotting-one.py > "$CODE_PATH"/output/lineage_one_wholetime.json
+PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/ClinMicro python "$CODE_PATH"/pathogens-portal-visualisations/ClinMicro/lineage-plotting-four.py > "$CODE_PATH"/output/lineage_four_recent.json
+PYTHONPATH="$CODE_PATH"/pathogens-portal-visualisations/ClinMicro python "$CODE_PATH"/pathogens-portal-visualisations/ClinMicro/lineage-plotting-five.py > "$CODE_PATH"/output/lineage_five_recent.json
 
 # Upload generated files
 for filename in $(ls $CODE_PATH/output) ; do