mamba

.gitignore

@@ -4,6 +4,6 @@
 .tools
 .pcks
 .rstats
-conda/
+mamba/
 data/
 *~

Makefile

@@ -1,31 +1,28 @@
 SHELL := /bin/bash
 
 # Targets
-TARGETS = .conda .mamba .tools .rstats .pcks .check
+TARGETS = .mamba .tools .rstats .pcks .check
 PBASE=$(shell pwd)
 
 all: ${TARGETS}
 
-.conda:
-	wget 'https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh' && bash Miniconda3-latest-Linux-x86_64.sh -b -p ${PBASE}/conda && rm -f Miniconda3-latest-Linux-x86_64.sh && touch .conda
+.mamba:
+	curl -L -O "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(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
 
-.mamba: .conda
-	export PATH=${PBASE}/conda/bin:${PATH} && conda install -y -n base -c conda-forge mamba && 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
 
-.tools: .conda .mamba
-	export PATH=${PBASE}/conda/bin:${PATH} && source activate base && 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
 
-.rstats: .conda .mamba .tools
-	export PATH=${PBASE}/conda/bin:${PATH} && source activate base && mamba install -y -c conda-forge -c bioconda bioconductor-genomicfeatures r-ggplot2 r-reshape2 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
 
-.pcks: .conda .mamba .tools .rstats
-	export PATH=${PBASE}/conda/bin:${PATH} && source activate base && 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
 
-.check: .conda .mamba .tools .rstats .pcks
-	export PATH=${PBASE}/conda/bin:${PATH} && source activate base && delly --version && touch .check
-
-download: .conda .mamba .tools .rstats .pcks
-	export PATH=${PBASE}/conda/bin:${PATH} && source activate base && cd data/ && gdown ${FILE} && tar -xzf sv.tar.gz && rm sv.tar.gz
+download: .mamba .tools .rstats .pcks
+	export PATH=${PBASE}/mamba/bin:${PATH} && cd data/ && gdown ${FILE} && tar -xzf sv.tar.gz && rm sv.tar.gz
 
 clean:
-	rm -rf $(TARGETS) $(TARGETS:=.o) conda/
+	rm -rf $(TARGETS) $(TARGETS:=.o) mamba/