This repo is dedicated to the updated version of the algorithm presented in the MLST.
The current projects include
data- Scripts for generating training and testing datatrain- Pytorch (lightning) code for training neural-networksdeploy- Triton wapper (hermes) code to deploy trained neural-networks
The repo includes implementation of both gwak1 and gwak2, where the configs for gwak1 live in the corresponding folder and in the Snakefile the corresponding rules have _gwak1.
The project uses uv, Conda and Snakemake to run the code. Follow installation instructions below to prepare your environment.
If you do not have Miniconda installed on your machine, follow first those steps
- use the
quickstartrepo to setupMiniconda
$ git clone git@github.com:ml4gw/quickstart.git
$ cd quickstart
$ make
If you see this error, it is already known in issue#7
Verifying checksum... Done.
Preparing to install helm into /you/path/miniconda3-tmp/bin/
helm installed into /you/path/miniconda3-tmp/bin//helm
helm not found. Is /you/path/miniconda3-tmp/bin/ on your $PATH?
Failed to install helm
For support, go to https://github.com/helm/helm.
make: *** [Makefile:65: install-helm] Error 1
do the following commands:
$ source ~/.bashrc
$ make install-poetry install-kubectl install-s3cmd
If everything was installed successfully, continue to the steps below.
If you do have Miniconda already installed on your machine, follow those steps
- checkout this repo and clone submodules (such as
ml4gw)
You might need to remove the base snakemake if you have one already.
$ curl -LsSf https://astral.sh/uv/install.sh | sh
$ uv python install 3.11
$ uv tool install snakemake==9.23.1
$ git clone git@github.com:ML4GW/gwak.git
$ cd gwak
$ snakemake -c1 gwak_init
After the initialization, you can check the path settings via snakemake -c1 gwak_info.
Now you are ready to gwak! You can run the training by doing
$ snakemake -c1 train_all
For testing by
$ snakemake -c1 scan_all
$ snakemake -c1 benchmark
Run with container.
$ snakemake -c1 build_containers
$ snakemake -c1 production_export
The result will from the container will redirect to GWAK_CONTAIN_OUTPUT_DIR.