Remove lsf references

PMBio · Apr 15, 2024 · e859885 · e859885
1 parent 8fa7a39
commit e859885
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diff --git 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
@@ -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
@@ -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: