Guide for leafcutter using conda installation

[Chunling Zhang]

Hi leafcutter developers,

I tried several methods (git clone, devtools using Rscripts, coda) on Linux to install the leafcutter packages, but fail to run leafcutter_ds.R due to R packages conflicts (Rcpp, optparse). It seems leafcutter was built on earlier R version but most dependencies were built on more recent R (4.0.3).

Do you have a guide for installation using conda to solve the R conflicts?

Your help is much appreciated.

Thanks,

Chunling 

[Ying J]

Hi Chunling,

I had the same issues as you and my lab mate(https://github.com/crotoc) helped me out, here is his recipe:

# please sub [xx] with your path
 conda create --prefix=[/opt/condaEnv/leafcutter]
source activate [/opt/condaEnv/leafcutter]
conda install r-base=3.6
conda install -c r r-rstan
conda install -c bioconda samtools
conda install -c bioconda regtools
conda install -c conda-forge r-devtools
 conda install -c bioconda bioconductor-biobase
conda install -c bioconda bioconductor-dirichletmultinomial
R -e 'devtools::install_github("davidaknowles/leafcutter/leafcutter")

Best,
Ying