Dependencies
- Linux system
- Conda and/or Docker
- Target files
- Mounted MiSeq (for method only)
Install pipeline
Conda method
The way I install conda:
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
bash miniconda.sh -b -p $HOME/miniconda
export PATH="$HOME/miniconda/bin:$PATH"
conda config --set always_yes yes
conda update -q conda
The easiest way to install sipprverse is to download the source code GitHub Link
git clone https://github.com/OLC-Bioinformatics/sipprverse.git
cd sipprverse
export PATH="/path/to/repository/sipprverse:$PATH"
conda env create -f environment.yml
source activate sipprverse
Docker method
Docker must already be installed
The docker image relies on conda to install all the dependencies, so the genesippr environment must be sourced within the container prior to launch. The supplied command below launches container, immediately sources the environment, and runs the pipeline, but it is also possible to run those commands separately from within the container. For additional details on the run command, please see the tutorial.
git clone https://github.com/OLC-Bioinformatics/sipprverse.git
cd sipprverse
docker build -t sipprverse:latest .
docker run -it --name sipprverse --rm sipprverse:latest /bin/bash -c "source activate genesippr && sippr.py -s /path/to/sequences -r /path/to/database"
Install targets (after pipeline is set-up)
source activate sipprverse
python -m databasesetup.database_setup -v -d /DESIRED/TARGET/PATH -s -c /PATH/TO/rMLST/CREDENTIALS