Installation

Installing Pandora

Install using pip

You can also install Pandora using the python package manager pip:

pip install git+https://github.com/tschuelia/Pandora.git

Please note that this can lead to issues with package versions and dependencies when installing in an existing (conda) environment. Verify the correct installation by running pandora -h.

Requirements

Pandora makes use of the Eigensoft software package, more specifically the smartpca and convertf tools. Before using Pandora, make sure you have smartpca and convertf installed. The easiest way to install Eigensoft is to use conda:

conda install eigensoft -c bioconda

If you don’t want to use conda, you can also follow the instructions in the linked Eigensoft repo.

Note that this won’t work if you are working on a MacBook with M1/M2 chip (OSX-ARM) just yet. See the Troubleshooting section below for instructions on how to deal with this.

Troubleshooting

Installing Eigensoft on MacBooks with M1/M2 chips

First of all, you should make sure that you are actually working on a MacBook with M1/M2 chip. You can do so by typing arch in your command line tool. If you see arm64 continue with the instructions below. Otherwise refer to the installation instructions above. Please make absolutely sure that you are on an M1/M2 Mac and you have no other option than to work on your Mac, because the following installation is a terrible hack. It works, but it’s ugly and every software engineer would (rightfully) get angry with me for even suggesting this solution ;-)

To install Eigensoft we will make use of micromamba and its platform tag. You will need conda for this.

  1. Install micromamba

conda install micromamba

  1. Create a new micromamba environment

micromamba env create -n eigensoft_env

  1. Install Eigensoft

micromamba install -n eigensoft_env eigensoft --platform osx-64

  1. Next, we need to find the directory where eigensoft was installed to. To do so, type

micromamba list -n eigensoft_env

  1. In the output you should see a line similar to this:

List of packages in environment: "/Users/julia/micromamba/envs/eigensoft_env"

6. Using the path that is stated there, we can manually concat the exec paths for smartpca and convertf by appending /bin/smartpca and /bin/convertf. So the full paths for smarptca and convertf will be something like

/Users/julia/micromamba/envs/eigensoft_env/bin/smartpca
/Users/julia/micromamba/envs/eigensoft_env/bin/convertf

7. Verify that the path is correct by typing them in your terminal one after the other. For convertf you should see an output with fatalx: and for smartpca something with no parameters. If the output says something about unknown command please open an issue and I’m sure we can figure out what is going wrong.

8. In the Pandora config file (see Usage for more details) make sure to set the options smartpca and convertf to the respective paths. So your config should then contain the following:

smartpca: /Users/julia/micromamba/envs/eigensoft_env/bin/smartpca
convertf: /Users/julia/micromamba/envs/eigensoft_env/bin/convertf

Error: too many open files

When running Pandora, especially when setting the number of replicates to a high number, you might see an error saying something like OSError: [Errno 24] Too many open files. You can fix this by increasing the number of allowed open files to e.g. 10000:

ulimit -n 10000

Especially with Apple MacBooks this number is typicall set very low per default.