- GitHub page: https://github.com/meganlsmith/delimitR
-
Download the version for your operating system e.g.
wget http://cmpg.unibe.ch/software/fastsimcoal26/downloads/fsc26_linux64.zip -
Unzip and then make executable with
chmod +x fsc26 -
See our conda_instructions.md (https://github.com/SmithsonianWorkshops/Species_Delimitation_2021_08/blob/main/conda_instructions.md) and create an environment just for delimitR.
-
If you are working on a linux system, there is a conda environment yml file here: https://github.com/SmithsonianWorkshops/Species_Delimitation_2021_08/blob/main/conda_environment_yml_files/delimitR_linux.yml (you can use this file to build a new environment with all dependencies with
conda env create --file delimitR_linux.yml) -
If you are working on a mac, there is a conda environment yml file here: https://github.com/SmithsonianWorkshops/Species_Delimitation_2021_08/blob/main/conda_environment_yml_files/delimitR_macos.yml (you can use this file to build a new environment with all dependencies with
conda env create --file delimitR_macos.yml) -
If you are not using a yml file, once you create a new environment, you will have to install the packages below via conda:
conda install -c conda-forge r-base
conda install python=2.7
conda install -c conda-forge r-devtools
conda install -c conda-forge r-stringi
conda install -c conda-forge r-stringr
conda install -c conda-forge r-knitr
conda install -c conda-forge r-rsqlite
conda install -c r r-dplyr
conda install -c conda-forge r-readr
conda install -c bioconda r-rematch2
conda install -c conda-forge r-sqldf
conda install -c r r-testthat
conda install -c conda-forge r-tibble
conda install -c conda-forge r-vroom
conda install -c conda-forge r-waldo
conda install -c conda-forge r-ranger
conda install -c conda-forge r-matrixstats
- Then download the delimitR code:
git clone https://github.com/meganlsmith/delimitR.git - Unpack the tar.gz file
- Set your working directory to the directory above the delimitR directory that was created when you unpacked the source code.
- Try typing
which Rto make sure it's the version you just installed with conda. - Start R by typing
R - Install one more dependency not available via conda:
install.packages("abcrf") - And then install delimitR from within R:
devtools::install('delimitR', dependencies = TRUE)