diff --git a/Jenkinsfile b/Jenkinsfile index cf5623a..065c86c 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -419,38 +419,6 @@ pipeline { } } } - - // Create a relative working directory and setup our - // data environment. - // Note: - // pathways2GO: v0.1.0 (not master) - // reactome: current/human - dir('./pathways2GO') { - git 'https://github.com/geneontology/pathways2GO.git' - - // Default namespace. - sh 'env' - - retry(3){ - // Get jar. - sh 'curl -O -L https://github.com/geneontology/pathways2GO/releases/download/v0.1.0/biopax2go.jar' - - // Biopax files needed - sh 'curl -O -L https://reactome.org/download/current/biopax.zip' - } - - // Ready. - sh 'unzip -o biopax.zip' - - // The actual command. - sh 'java -jar biopax2go.jar -b Homo_sapiens.owl -reacto ./reacto' - - // Make sure that we copy any files there, - // including the core dump of produced. - withCredentials([file(credentialsId: 'skyhook-private-key', variable: 'SKYHOOK_IDENTITY')]) { - sh 'scp -o StrictHostKeyChecking=no -o IdentitiesOnly=true -o IdentityFile=$SKYHOOK_IDENTITY -r ./reacto.owl skyhook@skyhook.berkeleybop.org:/home/skyhook/$BRANCH_NAME/ontology/extensions/reacto.owl' - } - } } } stage('Make Noctua GPAD') {