From 9f97f849c8242376af313903dade1abdebb86b57 Mon Sep 17 00:00:00 2001
From: Vitor Trovisco <vmt25@cam.ac.uk>
Date: Tue, 22 Dec 2020 17:03:23 +0000
Subject: [PATCH] Revert "Update weekly_routine.sh - testing replacing 'here'
marks (./) with the full filepath from root."
This reverts commit 884e76e836c2cdbe7f85b6a99cc69e55e78a2423
---
weekly_routine.sh | 10 +++++-----
1 file changed, 5 insertions(+), 5 deletions(-)
diff --git a/weekly_routine.sh b/weekly_routine.sh
index e36190d..d149e9c 100755
--- a/weekly_routine.sh
+++ b/weekly_routine.sh
@@ -209,7 +209,7 @@ if [[ -z "${DBNAME}" ]]; then
fi
# Transform $DBNAME
-CANTO_CONFIG="${CANTOSPACE}/canto/canto_deploy.yaml"
+CANTO_CONFIG="./canto/canto_deploy.yaml"
log "Inserting ${DBNAME} into ${CANTO_CONFIG}"
if [[ -e "${CANTO_CONFIG}" ]]; then
@@ -242,14 +242,14 @@ if [[ "${DATACHANGED}" == "YES" ]]; then
export OWLTOOLS_MEMORY=20g
# redo/replace merged FBbt-GO.obo ontology
- sh "${CANTOSPACE}/FBbt-GO_routine/FBbt-GO_routine.sh"
+ sh ./FBbt-GO_routine/FBbt-GO_routine.sh
# replace extension_config.tsv
- sh "${CANTOSPACE}/extension_config-Rscript/list-to-extension_config.sh"
+ sh ./extension_config-Rscript/list-to-extension_config.sh
# reload the ontologies and extension configuration
# JWRN comment: I suspect the sudo here is superfluous as the script is running as root so removed
- "${CANTOSPACE}/canto/script/canto_docker" "${CANTOSPACE}/script/canto_load.pl" --process-extension-config --ontology /import_export/FBbt-GO.obo --ontology /import_export/fly_development.obo --ontology /import_export/flybase_controlled_vocabulary.obo
+ ./canto/script/canto_docker ./script/canto_load.pl --process-extension-config --ontology /import_export/FBbt-GO.obo --ontology /import_export/fly_development.obo --ontology /import_export/flybase_controlled_vocabulary.obo
fi
# If DBNAME hasn't changed then restart canto and quit
@@ -283,7 +283,7 @@ if [[ ( -e "${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 ${JSONIMPORTFILE} into Canto"
- "${CANTOSPACE}/canto/script/canto_docker" "${CANTOSPACE}/script/canto_add.pl" --sessions-from-json "${JSONIMPORTFILE}" "ignore@flybase.org" 7227
+ ./canto/script/canto_docker ./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}"
--
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