PHRAPL_conda_install.md

Installing PHRAPL via conda

• Here are the official instructions: https://phrapl.github.io/Content/1.Installation.html#for-macos
• Note that the above instructinos require root privileges.
• Below, we have tried to build an environment (for Macs) for which you do not have to use sudo:

Mac-specific instructions

Create a Conda environment from a file we posted here to this GitHub repo:

conda env create -f https://raw.githubusercontent.com/SmithsonianWorkshops/Species_Delimitation_2021_08/main/conda_environment_yml_files/OX_env_phrapl.yml

Activate this environment:

conda activate OX_env_phrapl

Enter R to complete the last few installation steps:

R

In R, run these commands:

library(devtools)
devtools::install_url("https://cran.r-project.org/src/contrib/Archive/rPython/rPython_0.0-6.tar.gz", upgrade=FALSE)
devtools::install_url("https://cran.r-project.org/src/contrib/Archive/P2C2M/P2C2M_0.7.6.tar.gz", upgrade=FALSE)
devtools::install_github("bomeara/phrapl")

• The below may work on other systems:
• First, see our conda_instructions.md (https://github.com/SmithsonianWorkshops/Species_Delimitation_2021_08/blob/main/conda_instructions.md) and create an environment just for PHRAPL.
• This will avoid any dependency conflict with any other R installations you have.
• Next, install the necessary dependencies via conda:

conda install -c r r
conda install -c conda-forge r-devtools
conda install -c conda-forge r-ape
conda install -c conda-forge r-partitions
conda install -c r r-lattice
conda install -c conda-forge r-polynom
conda install -c conda-forge r-gmp
conda install -c r r-rgenoud
conda install -c conda-forge parallel
conda install -c conda-forge r-optimx
conda install -c r r-igraph
conda install -c conda-forge r-numderiv
conda install -c conda-forge r-nloptr
conda install -c conda-forge r-matrix
conda install -c r r-rcolorbrewer
conda install -c conda-forge r-binom
conda install -c conda-forge r-diagram
conda install -c r r-rjsonio
conda install -c conda-forge r-stringr
conda install -c conda-forge r-ggplot2
conda install python=2.7

• Download these libraries separately and unzip: wget https://github.com/ariadnamorales/phrapl-manual/blob/master/dependencies/rPython_0.0-6.tar.gz wget https://github.com/ariadnamorales/phrapl-manual/blob/master/dependencies/P2C2M_0.7.6.tar.gz

• If wget doesn't work on your system, download them directly from the GitHub site by clicking.

• Try typing which R to make sure it's the version you just installed with conda.

• Start R by typing R

• Install rPython: install.packages("rPython", repos=NULL)

• Install P2C2M: install.packages("P2C2M", repos=NULL)

• And then install PHRAPL from within R: devtools::install_github("bomeara/phrapl")