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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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install cnv_facets 0.16.0 with r-facets 0.6.1 using anaconda3 #35

Open jh2663 opened 3 years ago

jh2663 commented 3 years ago

Hi. thank you for your effort with this script. I am just wondering if there is a way of installing r-facets 0.6.1 version with the 0.16.0 version of cnv_facets using conda or mamba command in linux system. I find r-facets 0.6.1 is only installable in R >=4.0 while cnv_facets is only for 3.5 or 3.6?

Best,

dariober commented 3 years ago

Hi- sorry about that. I need to revise the installation recipe to update it to work with more recent versions. For the time being, the following should work, but I haven't tested it yet.

Skip the bioconda installation but use conda to install the dependencies. So something like:

conda create -n cnv_facets
conda activate cnv_facets

# I recommend switching from `conda install` to `mamba install` for good
mamba install 'r-facets>=0.6.1' 'r-data.table' 'r-ggplot2' 'r-argparse>=2' 'snp-pileup>=0.6.1' 'r-gridextra' 'bioconductor-rsamtools' 'samtools' 'bcftools >=1.9'

Now download the script cnv_facets.R and put it on your PATH:

mkdir -p $PREFIX/bin

curl -s https://raw.githubusercontent.com/dariober/cnv_facets/master/bin/cnv_facets.R > $PREFIX/bin/cnv_facets.R
chmod a+x $PREFIX/bin/cnv_facets.R