names are hard; work on #158

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=$SKYHOOK_IDENTITY -r ./reacto.owl [email protected]:/home/skyhook/$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=$SKYHOOK_IDENTITY -r ./reacto.owl [email protected]:/home/skyhook/$BRANCH_NAME/ontology/extensions/'
 		    }
 		}
 	    }