README.md

hybsearch

A tool to find nonmonophyly in a phylogenetic tree.

To Install

• install docker: docker.com or brew install docker-ce (with https://brew.sh installed)

To Run

Two steps:

1. Either double-click the "hybsearch" file in the folder, or, with a terminal, cd into the hybsearch folder and run ./hybsearch.
2. Run docker run -p 8080:8080 -it hybsearch/hybsearch

If you don't have docker, TODO.

If you're on Windows, TODO.

To Develop

You'll need Docker, still.

For the Electron app

Any changes you make to the JS can be run by simply pressing ⌘R. There is no build process.

For the Docker container / data pipeline

Whenever you change the data pipeline, you will need to rebuild the Docker image.

We recommend using a local Docker tag to test with; anywhere you would write hybsearch/hybsearch, you should just write hybsearch instead.

To rebuild the container:

docker build -t hybsearch .

To run your rebuilt container:

docker run -p 8080:8080 -it hybsearch

Miscallaneous Bits

Dependencies

Our current versions of our dependencies:

• Docker: 17.20.x

Or

• Node: 8.x
• Beagle: 2.1.2
• OpenMPI: 2.1.1
• Clustal-Omega: 1.2.0
• MrBayes: 3.2.6
• Electron: 1.6.10
• seq-gen: 1.3.3
• seqmagick: 0.6.1

If you have Docker installed, all you need to do is (in the project root)

$ docker run --port 8080:8080 -it hybsearch/hybsearch
$ ./hybsearch

which will start the server that the electron app uses.

To convert files:

./vendor/seqmagick/cli.py convert --input-format fasta --output-format nexus --alphabet dna <input> <output>

How to update Electron:

• npm install -g electron-download
• electron-download --version=<version>
• Copy the zip from ~/.electron and extract it into hybsearch/vendor
• Edit the hybsearch file to point to the new path
• Remove the old folder

Some HammingDistance Notes:

>>> hamming-distance speciesA speciesB
$minimumDistance
>>> estimate-generations $minimumDistance
{divergenceTime, generationCount}
>>> seq-gen $file --generations $generationCount
$sequences > sequences.fasta
>>> hamdis sequences.fasta
???