Update weekly_routine.sh - testing replacing 'here' marks (./) with the full filepath from root.

weekly_routine.sh

@@ -209,7 +209,7 @@ if [[ -z "${DBNAME}" ]]; then
 fi
 
 # Transform $DBNAME 
-CANTO_CONFIG="./canto/canto_deploy.yaml"
+CANTO_CONFIG="${CANTOSPACE}/canto/canto_deploy.yaml"
 log "Inserting ${DBNAME} into ${CANTO_CONFIG}"
 
 if [[ -e "${CANTO_CONFIG}" ]]; then
@@ -242,14 +242,14 @@ if [[ "${DATACHANGED}" == "YES" ]]; then
     export OWLTOOLS_MEMORY=20g
 
     # redo/replace merged FBbt-GO.obo ontology
-    sh ./FBbt-GO_routine/FBbt-GO_routine.sh
+    sh "${CANTOSPACE}/FBbt-GO_routine/FBbt-GO_routine.sh"
 
     # replace extension_config.tsv
-    sh ./extension_config-Rscript/list-to-extension_config.sh
+    sh "${CANTOSPACE}/extension_config-Rscript/list-to-extension_config.sh"
 
     # reload the ontologies	and extension configuration
     # JWRN comment: I suspect the sudo here is superfluous as the script is running as root so removed
-    ./canto/script/canto_docker ./script/canto_load.pl --process-extension-config --ontology  /import_export/FBbt-GO.obo --ontology    /import_export/fly_development.obo --ontology   /import_export/flybase_controlled_vocabulary.obo
+    "${CANTOSPACE}/canto/script/canto_docker" "${CANTOSPACE}/script/canto_load.pl" --process-extension-config --ontology  /import_export/FBbt-GO.obo --ontology    /import_export/fly_development.obo --ontology   /import_export/flybase_controlled_vocabulary.obo
 fi
 
 # If DBNAME hasn't changed then restart canto and quit
@@ -283,7 +283,7 @@ if [[ ( -e "${CURATEDPAPERLISTFILE}" ) && ( -s "${CURATEDPAPERLISTFILE}" ) ]]; t
     # VT comment: this next step make take some time, depending on the amount of new data
     # JWRN comment: again I suspect the sudo is superfluous so removed
     log "Importing ${JSONIMPORTFILE} into Canto"
-    ./canto/script/canto_docker ./script/canto_add.pl --sessions-from-json "${JSONIMPORTFILE}" "ignore@flybase.org" 7227
+    "${CANTOSPACE}/canto/script/canto_docker" "${CANTOSPACE}/script/canto_add.pl" --sessions-from-json "${JSONIMPORTFILE}" "ignore@flybase.org" 7227
 
     # remove the fbrf_input_list.tsv file once done, so that the script doesn't try to add the same information again next time its run
     #/bin/rm "${CURATEDPAPERLISTFILE}"