diff --git a/docs/seed_gene_discovery.md b/docs/seed_gene_discovery.md index c0fefda9..c58183ab 100644 --- a/docs/seed_gene_discovery.md +++ b/docs/seed_gene_discovery.md @@ -2,7 +2,7 @@ This pipeline discovers *seed genes* for DeepRVAT training. The pipeline runs SKAT and burden tests for missense and pLOF variants, weighting variants with Beta(MAF,1,25). To run the tests, we use the `Scoretest` from the [SEAK](https://github.com/HealthML/seak) package (has to be installed from github). -To run the pipeline, an experiment directory with the `config.yaml` has to be created. An `lsf.yaml` file specifiying the compute resources for each rule in `seed_gene_discovery.snakefile` might also be needed depending on your system (see as an example the `lsf.yaml` file in this directory). +To run the pipeline, an experiment directory with the `config.yaml` has to be created. ## Input data diff --git a/pipelines/association_testing/burdens.snakefile b/pipelines/association_testing/burdens.snakefile index a585d422..5ac7cf1f 100644 --- a/pipelines/association_testing/burdens.snakefile +++ b/pipelines/association_testing/burdens.snakefile @@ -79,7 +79,7 @@ rule compute_burdens: prefix = '.' threads: 8 resources: - mem_mb = 2000000, # Using this value will tell our modified lsf.profile not to set a memory resource + mem_mb = 20000, load = 8000, gpus = 1 shell: diff --git a/pipelines/training/train.snakefile b/pipelines/training/train.snakefile index 2915c6ae..4c0b9433 100644 --- a/pipelines/training/train.snakefile +++ b/pipelines/training/train.snakefile @@ -57,7 +57,7 @@ rule train: prefix = '.', priority: 1000 resources: - mem_mb = 2000000, # Using this value will tell our modified lsf.profile not to set a memory resource + mem_mb = 20000, load = 8000, gpus = 1 shell: