2.2.2: install R package fix

friendsofstrandseq · Sep 22, 2023 · bf295e4 · bf295e4
1 parent 0f4ef95
commit bf295e4
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 5 deletions.
diff --git a/github-actions-runner/docker_procedure.md b/github-actions-runner/docker_procedure.md
@@ -46,4 +46,4 @@ snakemake --configfile .tests/config/simple_config.yaml --config ashleys_pipelin
 
 docker login -u weber8thomas
 docker build --platform=linux/amd64 -t weber8thomas/mosaicatcher-pipeline:VERSION .
-docker push -t weber8thomas/mosaicatcher-pipeline:VERSION
+docker push weber8thomas/mosaicatcher-pipeline:VERSION
diff --git a/workflow/rules/setup.smk b/workflow/rules/setup.smk
@@ -18,11 +18,10 @@ rule install_BSgenome_package:
             config["reference"]
         ),
     params:
-        selected_package=lambda wc, input: "BSgenome.Hsapiens.UCSC.{}".format(
+        selected_package=lambda wc, input: "BSgenome.{}.UCSC.{}".format(
+            "Mmusculus" if config["reference"] == "mm10" else "Hsapiens",
             config["reference"]
-        )
-        if config["reference"] in ["hg38", "hg19", "mm10"]
-        else input.package,
+        ) if config["reference"] in ["hg38", "hg19", "mm10"] else input.package,
     conda:
         "../envs/rtools.yaml"
     resources: