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4 changes: 2 additions & 2 deletions docs/setup.md
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# 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

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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')"
```
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