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cluster.json
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cluster.json
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{
"__default__": {
"queue": "highp",
"memory": "2G",
"name": "{rule}.{wildcards.experiment}",
"output": "/u/project/ernst/skwon94/pairwise_scoring/logs/{rule}.{wildcards.experiment}.out",
"time": "0:30:00",
"threads": 1
},
"generate_windows": {
"name": "{rule}",
"output": "/u/project/ernst/skwon94/pairwise_scoring/logs/{rule}.out"
},
"generate_data": {
"memory": "4G",
"name": "{rule}.{wildcards.chrom}",
"output": "/u/project/ernst/skwon94/pairwise_scoring/logs/{rule}.{wildcards.chrom}.out",
"time": "4:00:00",
"threads": 2
},
"hyperparam_search": {
"memory": "8G",
"name": "{rule}.{wildcards.classifier}.{wildcards.heldout_chroms}.{wildcards.dist}.{wildcards.seed}",
"output": "/u/project/ernst/skwon94/pairwise_scoring/logs/{rule}.{wildcards.classifier}.{wildcards.heldout_chroms}.{wildcards.dist}.{wildcards.seed}.out",
"time": "12:00:00",
"threads": 4
},
"train": {
"memory": "12G",
"name": "{rule}.{wildcards.classifier}.{wildcards.heldout_chroms}.{wildcards.dist}.{wildcards.seed}",
"output": "/u/project/ernst/skwon94/pairwise_scoring/logs/{rule}.{wildcards.classifier}.{wildcards.heldout_chroms}.{wildcards.dist}.{wildcards.seed}.out",
"time": "12:00:00",
"threads": 4
},
"eval_jaccard": {
"memory": "1G",
"name": "{rule}.{wildcards.heldout_chroms}.{wildcards.dist}",
"output": "/u/project/ernst/skwon94/pairwise_scoring/logs/{rule}.{wildcards.heldout_chroms}.{wildcards.dist}.out",
"time": "2:00:00",
"threads": 4
},
"predict": {
"memory": "1G",
"name": "{rule}.{wildcards.classifier}.{wildcards.chrom}.{wildcards.dist}",
"output": "/u/project/ernst/skwon94/pairwise_scoring/logs/{rule}.{wildcards.classifier}.{wildcards.chrom}.{wildcards.dist}.out",
"time": "8:00:00",
"threads": 4
},
"eval_classifier": {
"memory": "1G",
"name": "{rule}.{wildcards.classifier}.{wildcards.heldout_chroms}.{wildcards.dist}",
"output": "/u/project/ernst/skwon94/pairwise_scoring/logs/{rule}.{wildcards.classifier}.{wildcards.heldout_chroms}.{wildcards.dist}.out",
"time": "8:00:00",
"threads": 4
},
"eval_classifier_ensemble": {
"memory": "1G",
"name": "{rule}.{wildcards.classifier}.{wildcards.heldout_chroms}.{wildcards.dist}",
"output": "/u/project/ernst/skwon94/pairwise_scoring/logs/{rule}.{wildcards.classifier}.{wildcards.heldout_chroms}.{wildcards.dist}.out",
"time": "8:00:00",
"threads": 4
},
"eval_classifier_ensemble_smooth": {
"memory": "1G",
"name": "{rule}.{wildcards.classifier}.{wildcards.heldout_chroms}.{wildcards.dist}",
"output": "/u/project/ernst/skwon94/pairwise_scoring/logs/{rule}.{wildcards.classifier}.{wildcards.heldout_chroms}.{wildcards.dist}.out",
"time": "8:00:00",
"threads": 4
},
"jaccard": {
"memory": "1G",
"name": "{rule}.{wildcards.chrom}.{wildcards.dist}",
"output": "/u/project/ernst/skwon94/pairwise_scoring/logs/{rule}.{wildcards.chrom}.{wildcards.dist}.out",
"time": "4:00:00",
"threads": 4
},
"sort_bedpe": {
"name": "{rule}.{wildcards.method}",
"output": "/u/project/ernst/skwon94/pairwise_scoring/logs/{rule}.{wildcards.method}.out",
"time": "8:00:00",
"threads": 8
},
"smooth_bedpe": {
"memory": "4G",
"name": "{rule}.{wildcards.method}.{wildcards.chrom}",
"output": "/u/project/ernst/skwon94/pairwise_scoring/logs/{rule}.{wildcards.method}.{wildcards.chrom}.out",
"time": "12:00:00"
},
"run_juicer_pre": {
"memory": "8G",
"name": "{rule}.{wildcards.method}",
"output": "/u/project/ernst/skwon94/pairwise_scoring/logs/{rule}.{wildcards.method}.out",
"time": "4:00:00"
},
"report_hic": {
"name": "{rule}.{wildcards.chrom}.{wildcards.norm}",
"output": "/u/project/ernst/skwon94/pairwise_scoring/logs/{rule}.{wildcards.chrom}.{wildcards.norm}.out",
"time": "4:00:00",
"memory": "16G"
},
"aggregate_hic": {
"name": "{rule}.{wildcards.norm}",
"output": "/u/project/ernst/skwon94/pairwise_scoring/logs/{rule}.{wildcards.norm}.out",
"time": "8:00:00",
"threads": 4,
"memory": "2G"
}
}