1.0.4 • Published 6 years ago
hybsearch-cli v1.0.4
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:
- Either double-click the "hybsearch" file in the folder, or, with a terminal,
cd
into the hybsearch folder and run./hybsearch
. - 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 intohybsearch/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
???