Add dependencies and memory requirement

PejLab · May 6, 2024 · 36e5369 · 36e5369
1 parent e9c4d8e
commit 36e5369
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diff --git a/Pheast/environment.yml b/Pheast/environment.yml
@@ -7,8 +7,13 @@ dependencies:
   - bioconductor-impute
   - bioconductor-qvalue
   - bioconductor-variantannotation
+  - dask<2024.2
+  - pandas
+  - pandas-plink
   - pip
   - plink2=2
+  - r-glmnet
+  - r-optparse
   - rpy2
   - snakemake
   - pip:

diff --git a/Pheast/steps/covariates.smk b/Pheast/steps/covariates.smk
@@ -40,6 +40,8 @@ rule covariates:
     params:
         n_geno_pcs = 5,
         n_pheno_pcs = 20,
+    resources:
+        mem_mb = 16000,
     shell:
         """
         Rscript scripts/covariates.R \