install_conda_env.sh

echo "note: r-seurat is listed here but does not actually work"

conda create -n glia_paper -c conda-forge -c bioconda -c jluquette -c dranew -c soil bcftools bedtools bioconductor-annotationdbi bioconductor-annotationfilter bioconductor-biovizbase bioconductor-bsgenome bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 bioconductor-bsgenome.hsapiens.ucsc.hg19 bioconductor-bsgenome.hsapiens.ucsc.hg38 bioconductor-genomeinfodb bioconductor-genomeinfodbdata bioconductor-genomicalignments bioconductor-genomicfeatures bioconductor-genomicranges bioconductor-gviz bioconductor-txdb.hsapiens.ucsc.hg19.knowngene bioconductor-variantannotation bx-python mscorefonts pandas r-argparse r-curl r-devtools r-extrafont r-extrafontdb r-harmonicmeanp r-kernsmooth r-lme4 r-lmertest r-nnls r-openxlsx r-pheatmap r-rcolorbrewer r-readxl r-rttf2pt1 r-svglite s3transfer scan2 ucsc-bedgraphtobigwig ucsc-bigwigaverageoverbed r-r.matlab bioconductor-dnacopy bioconductor-ctc r-inline r-fastcluster r-heatmap3 r-rio vcf2maf vcflib r-seurat


echo "INSTALL MANUALLY: r-mutenrich, r-scan2 (if updated)"