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fix channels
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tobiasrausch committed Oct 24, 2024
1 parent 2e6916c commit cfbc47d
Showing 1 changed file with 2 additions and 2 deletions.
4 changes: 2 additions & 2 deletions Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,10 @@ PBASE=$(shell pwd)
all: ${TARGETS}

.mamba:
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
curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(shell uname)-$(shell uname -m).sh" && bash Miniforge3-$(shell uname)-$(shell uname -m).sh -b -p mamba && rm "Miniforge3-$(shell uname)-$(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 --override-channels -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
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