Merge branch 'vitor_testing' into 'testing'

merging vitor_testing into testing

See merge request !9

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 "${CANTO_CONFIG}" ]]; then
@@ -242,10 +242,10 @@ if [[ "${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
@@ -267,7 +267,7 @@ check_if_canto_restart_required
 CURATEDPAPERLISTFILE="./fbrf_input_list.tsv"
 
 log "Creating ${CURATEDPAPERLISTFILE}"
-/usr/bin/perl /data/export/support_scripts/get_fbrfs_to_add_to_canto.pl /data/export/support_scripts/modules_server.cfg > "${CURATEDPAPERLISTFILE}"
+#/usr/bin/perl /data/export/support_scripts/get_fbrfs_to_add_to_canto.pl /data/export/support_scripts/modules_server.cfg > "${CURATEDPAPERLISTFILE}"
 
 # Test fbrf_input_list.tsv exists and isn't empty
 if [[ ( -e "${CURATEDPAPERLISTFILE}" ) && ( -s "${CURATEDPAPERLISTFILE}" ) ]]; then