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tkdagdelen / gnocchi_old

Apache License 2.0
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Evaluation: Add flags to CLI to do k-fold cross-validation #40

Open tkdagdelen opened 7 years ago

tkdagdelen commented 7 years ago

https://github.com/tkdagdelen/gnocchi/blob/evaluation/gnocchi-cli/src/main/scala/net/fnothaft/gnocchi/cli/EvaluateModel.scala#L136

tkdagdelen commented 7 years ago

./bin/gnocchi-submit --conf spark.kryoserializer.buffer.max=1m --master yarn-client --num-executors 60 --executor-cores 2 --executor-memory 20g -- EvaluateModel /data/52409/decrypted/GenotypeFiles/sub/sub20131107/iid_SSRIdbGaP.vcf /data/52409/decrypted/PhenotypeFiles/fixed_phs000670.v1.pht003556.v1.p1.c1.PGRN_AMPS_Subject_Phenotypes.HMB.pheno.txt ADDITIVE_LOGISTIC /data/patrick/TestDataResults 10_121180103_G,6_78407561_A,11_78994647_A,6_78671581_A,6_78408635_A /data/patrick/evalResults -saveAsText -phenoName remissionqids.w8 -covar -covarFile /data/52409/decrypted/PhenotypeFiles/fixed_phs000670.v1.pht003556.v1.p1.c1.PGRN_AMPS_Subject_Phenotypes.HMB.covar.txt -covarNames EVEC.1,EVEC.2,EVEC.3,EVEC.4 -overwriteParquet -oneTwo