diff --git a/Makefile b/Makefile index 5a77f4a..6000840 100644 --- 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 index 93e03f6..9f077a4 100644 --- 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