diff --git a/Jenkinsfile b/Jenkinsfile index 54352fc..7671187 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -409,6 +409,38 @@ 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') {