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@tobiasrausch
tobiasrausch committed Apr 19, 2024
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2 changes: 1 addition & 1 deletion Makefile
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Expand Up @@ -13,7 +13,7 @@ all: ${TARGETS}
export PATH=${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 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
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