small updates to prepare singularity for the cluster

Snakefile

@@ -34,7 +34,7 @@ localrules:
     generate_exclude_file_2,
     link_normalized_info_file,
     prepare_segments,
-    install_StrandPhaseR,
+    split_external_snv_calls,
     prepare_strandphaser_config_per_chrom
 
 rule all:

run_pipeline_cluster-singularity.sh

 #!/bin/bash
 
+# Set these two paths to link large external data (reference genomes) to the respective places within the image
 REF="/g/korbel/shared/datasets/refgenomes/human/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna"
+R_REF="/g/korbel/meiers/R-lib/3.4.0-foss-2016b/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit"
 
 snakemake \
     -j 100 \
     --configfile Snake.config-singularity.json \
     --use-singularity \
-	--singularity-args "-B ${REF}:/reference.fa:ro -B ${REF}.fai:/reference.fa.fai:ro" \
+	--singularity-args "-B ${REF}:/reference.fa:ro \
+                        -B ${REF}.fai:/reference.fa.fai:ro \
+                        -B ${R_REF}:/usr/local/lib/R/site-library/BSgenome.Hsapiens.UCSC.hg38/extdata/single_sequences.2bit:ro" \
 	--cluster-config cluster.json \
     --local-cores 8 \
     --cluster "sbatch -o slurm/{rule}.%j.log -e slurm/{rule}.%j.log --cpus-per-task {cluster.n} --time {cluster.time} --mem {cluster.mem}" \