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weizhouUMICH / SAIGE

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How to use docker with SAIGE-GENE? #298

Closed garyzhubc closed 2 years ago

garyzhubc commented 3 years ago

I have my files stored at /Users/garyzhubc/Desktop but I couldn't locate these files as input when I do: 

docker exec -w /Users/garyzhubc/Desktop d7501bd45226 /usr/local/bin/step2_SPAtests.R \
  --bgenFile=ukb_imp_chr1_v3_pruned_reduced.bgen \
  --bgenFileIndex=ukb_imp_chr1_v3_pruned_reduced.bgen.bgi \
  --sampleFile=ukb_imp_chr1_v3_pruned_reduced.sample \
  --chrom=1 \
  --minMAF=0 \
  --minMAC=0.5 \
  --maxMAFforGroupTest=0.01 \
  --GMMATmodelFile=./output/example_quantitative.rda \
  --varianceRatioFile=./output/example_quantitative_cate.varianceRatio.txt \
  --SAIGEOutputFile=./output/example_quantitative.SAIGE.gene.txt \
  --numLinesOutput=1 \
  --groupFile=group_file.tsv \
  --sparseSigmaFile=./output/example_quantitative_cate.varianceRatio.txt_relatednessCutoff_0.125_2000_randomMarkersUsed.sparseSigma.mtx \
  --IsSingleVarinGroupTest=TRUE \
  --LOCO=FALSE
weizhouUMICH commented 2 years ago

You will need mount the external folder to the docker container in order to access the files.