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tobiasrausch · Jun 16, 2024 · 179b546 · 179b546
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diff --git a/Makefile b/Makefile
@@ -10,19 +10,19 @@ all: ${TARGETS}
 	curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(shell uname)-$(shell uname -m).sh" && bash Mambaforge-$(shell uname)-$(shell uname -m).sh -b -p mamba && rm "Mambaforge-$(shell uname)-$(shell uname -m).sh" && touch .mamba
 
 .tools: .mamba
-	export PATH=${PBASE}/mamba/bin:${PATH} && mamba install -y -c conda-forge -c bioconda datamash samtools bcftools bedtools htslib bwa delly alfred freebayes igv wally minimap2 && touch .tools
+	export PATH="${PBASE}/mamba/bin:${PATH}" && mamba install -y -c conda-forge -c bioconda datamash samtools bcftools bedtools htslib bwa delly alfred freebayes igv wally minimap2 && touch .tools
 
 .rstats: .mamba .tools
-	export PATH=${PBASE}/mamba/bin:${PATH} && mamba install -y -c conda-forge -c bioconda bioconductor-genomicfeatures r-ggplot2 r-reshape2 r-gridextra r-cowplot bioconductor-dnacopy && touch .rstats
+	export PATH="${PBASE}/mamba/bin:${PATH}" && mamba install -y -c conda-forge -c bioconda bioconductor-genomicfeatures r-ggplot2 r-reshape2 r-gridextra r-cowplot bioconductor-dnacopy && touch .rstats
 
 .pcks: .mamba .tools .rstats
-	export PATH=${PBASE}/mamba/bin:${PATH} && mamba install -y -c conda-forge -c bioconda cyvcf2 numpy pysam && pip install gdown && touch .pcks
+	export PATH="${PBASE}/mamba/bin:${PATH}" && mamba install -y -c conda-forge -c bioconda cyvcf2 numpy pysam && pip install gdown && touch .pcks
 
 .check: .mamba .tools .rstats .pcks
-	export PATH=${PBASE}/mamba/bin:${PATH} && delly --version && touch .check
+	export PATH="${PBASE}/mamba/bin:${PATH}" && delly --version && touch .check
 
 download: .mamba .tools .rstats .pcks
-	export PATH=${PBASE}/mamba/bin:${PATH} && cd data/ && gdown ${FILE} && tar -xzf sv.tar.gz && rm sv.tar.gz
+	export PATH="${PBASE}/mamba/bin:${PATH}" && cd data/ && gdown ${FILE} && tar -xzf sv.tar.gz && rm sv.tar.gz
 
 clean:
 	rm -rf $(TARGETS) $(TARGETS:=.o) mamba/
diff --git a/README.md b/README.md
@@ -20,17 +20,6 @@ Download the course data:
 
 `make FILE=1nxzjQFt33ch1P_nWF66q1tkHv5gxTaKb download`
 
-## Installation - Mac OS
-
-Load the conda environment with all required tools
-
-`conda env create -f environment.yml`
-
-Download and unpack the course data
-
-`cd data/ && gdown 1nxzjQFt33ch1P_nWF66q1tkHv5gxTaKb && tar -xzf sv.tar.gz && rm sv.tar.gz`
-
-
 ## Load the software stack
 
 Load the mamba environment with all required tools