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Getting started
git clone https://github.com/bioforensics/yeat.git
cd yeat
conda env create -f environment.yml
conda create -n yeat-metaMDBG -c bioconda "metamdbg>=1.0" -y
conda create -n yeat-velvet -c bioconda "perl-velvetoptimiser>=2.2" -y
conda activate yeat
pip install .
Users on other operating systems, such as macOS, will need to manually install a few packages by building them from source, as not all required packages are available via Anaconda.
In order to run Bandage in YEAT's workflow, users will need to manually download the pre-built binaries files here or build it from the source code here. Instructions for building Bandage from the source code can be found here.
Once the binary file has been obtained, users will need to update their environment's $PATH to include the path to the directory containing the binary file.
Example for MacOS:
export PATH=~/projects/Bandage/Bandage.app/Contents/MacOS:$PATH
In order to run the pre-built binary files successfully, ensure that the binary file is kept in the same directory with all of the other files that came with it.
yeat-auto short_reads --files {short_read1} {short_read2} > config.cfg
yeat --outdir {path} config.cfg
Run a simple YEAT job without a configuration file for paired-end reads only:
just-yeat-it --outdir {path} {short_read1} {short_read2}