From 42222dd93612f1a2411f1c0fd73d2def03802f98 Mon Sep 17 00:00:00 2001 From: Seth Carbon Date: Wed, 29 Jan 2020 15:04:27 -0800 Subject: [PATCH] names are hard; work on #158 --- Jenkinsfile | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/Jenkinsfile b/Jenkinsfile index eea8410..f7a47a0 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -402,26 +402,27 @@ pipeline { 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' - sh 'unzip -o biopax.zip' + } - // Fake Catalog. - sh 'touch catalog-v001-for-noctua.xml' + // Ready. + sh 'unzip -o biopax.zip' - // The actual command. - //sh 'java -jar biopax2go.jar -b Homo-sapiens.owl -reacto ./REACTO -c catalog-v001-for-noctua.xml -lego http://skyhook.berkeleybop.org/issue-158-reactome-ontology/ontology/extensions/go-lego.owl' - sh 'java -jar biopax2go.jar -b Homo_sapiens.owl -reacto ./reacto.owl -lego http://current.geneontology.org/ontology/extensions/go-lego.owl' + // Need fake catalog. + sh 'touch catalog-v001-for-noctua.xml' - // 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/' - } + // The actual command. + //sh 'java -jar biopax2go.jar -b Homo-sapiens.owl -reacto ./REACTO -c catalog-v001-for-noctua.xml -lego http://skyhook.berkeleybop.org/issue-158-reactome-ontology/ontology/extensions/go-lego.owl' + sh 'java -jar biopax2go.jar -b Homo_sapiens.owl -reacto ./reacto -lego http://current.geneontology.org/ontology/extensions/go-lego.owl' + + // 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/' } } }