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remove unnecessary reacto.owl stanza; likely echoes from fixes for #35
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kltm committed Jun 26, 2020
1 parent eb69c1c commit 9edb178
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Original file line number Diff line number Diff line change
Expand Up @@ -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=$SKYHOOK_IDENTITY -r ./reacto.owl [email protected]:/home/skyhook/$BRANCH_NAME/ontology/extensions/reacto.owl'
}
}
}
}
stage('Make Noctua GPAD') {
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