From b4bb2f22e20095400243bb757aa225e40ea44b9a Mon Sep 17 00:00:00 2001 From: caufieldjh Date: Wed, 4 Sep 2024 13:59:04 -0400 Subject: [PATCH] Remove output_dir value since it's using the default anyway --- Jenkinsfile | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/Jenkinsfile b/Jenkinsfile index 2559e5f..1e211e9 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -74,7 +74,8 @@ pipeline { dir('./gitrepo') { script { // Get the names of all BioPortal ontologies - sh ". venv/bin/activate && kgbioportal get-ontology-list --api_key ${NCBO_API_KEY} --output_dir data/raw/" + // This saves the list to data/raw/ontologylist.tsv + sh ". venv/bin/activate && kgbioportal get-ontology-list --api_key ${NCBO_API_KEY}" // Now download all // or at least in the future, do them all. @@ -82,7 +83,8 @@ pipeline { sh "printf 'ENVO\nPO\nSEPIO\n' > data/raw/ontologylist.tsv" // Download the ontologies - sh ". venv/bin/activate && kgbioportal download --api_key ${NCBO_API_KEY} --ontology_file data/raw/ontologylist.tsv --output_dir data/raw/" + // This saves them to data/raw/ + sh ". venv/bin/activate && kgbioportal download --api_key ${NCBO_API_KEY} --ontology_file data/raw/ontologylist.tsv" } }