diff --git a/docs/setup.md b/docs/setup.md index 0feb7df..fa03453 100644 --- a/docs/setup.md +++ b/docs/setup.md @@ -1,6 +1,6 @@ # Getting started -Baltica comprise of a collection of workflows and analysis scripts. Workflows are powered by [Snakemake](https://snakemake.readthedocs.io/en/stable/) [^1]. Analysis are done with the Rlang. Bellow we document how to obtain install the methods on which Baltica depends. +Baltica is comprised of a collection of workflows and analysis scripts. Workflows are powered by [Snakemake](https://snakemake.readthedocs.io/en/stable/) [^1]. Analysis are done with the Rlang. Below we document how to obtain and install the methods on which Baltica depends. ## Install miniconda @@ -66,7 +66,7 @@ conda create --name leafcutter python=2.7 --yes conda activate leafcutter conda install -c bioconda samtools r-base=3.6 --yes -Rscript -e "install.packages('devtools', repos='http://cran.us.r-project.org', dependencies=TRUE)" +Rscript -e "install.packages('devtools', repos='http://cran.us.r-project.org',warning dependencies=TRUE)" Rscript -e "Sys.setenv(TAR = '/bin/tar'); devtools::install_github('stan-dev/rstantools')" Rscript -e "Sys.setenv(TAR = '/bin/tar'); devtools::install_github('davidaknowles/leafcutter/leafcutter')" ```