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remove unnecessary reacto.owl stanza; likely echoes from fixes for #35
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@@ -419,38 +419,6 @@ pipeline { | |
} | ||
} | ||
} | ||
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// 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' | ||
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// Default namespace. | ||
sh 'env' | ||
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retry(3){ | ||
// Get jar. | ||
sh 'curl -O -L https://github.com/geneontology/pathways2GO/releases/download/v0.1.0/biopax2go.jar' | ||
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// Biopax files needed | ||
sh 'curl -O -L https://reactome.org/download/current/biopax.zip' | ||
} | ||
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// Ready. | ||
sh 'unzip -o biopax.zip' | ||
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// The actual command. | ||
sh 'java -jar biopax2go.jar -b Homo_sapiens.owl -reacto ./reacto' | ||
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// 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/reacto.owl' | ||
} | ||
} | ||
} | ||
} | ||
stage('Make Noctua GPAD') { | ||
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