Installation
weave is a stand alone python script that triggers execution of containerized subjobs defined in the workflow. weave does require a few dependencies currently, with plans to dwindle these requirements in the future.
Setup¶
Warning
All requirements should be installed to a python virtual environment and not to the system python
# clone repo
git clone https://github.com/OpenOmics/weave.git
cd weave
# create virtual environment
python -m venv ~/.my_venv
# activate environment
source ~/.my_venv/bin/activate
pip install -r requirements.txt
Snakemake & singularity¶
Note
Additional requirements beyond those listed in requirements.txt are the Snakemake python package and the singularity containerization software
On NIH servers¶
Biowulf uses environmental modules to control software. After executing the above you should see a message similar to:
[+] Loading snakemake 7.XX.X on cnXXXX
[+] Loading singularity 4.X.X on cnXXXX
Bigsky uses spack to load modules so a consolidated conda environment with snakemake is activated:
if [ ! -x "$(command -v "snakemake")" ]; then
source /gs1/apps/user/rmlspack/share/spack/setup-env.sh
export PS1="${PS1:-}"
spack load -r miniconda3@4.11.0/y4vyh4u
source activate snakemake7-19-1
fi
# Add this folder to $PATH
export PATH="/gs1/RTS/OpenOmics/bin:${PATH}"
# Add different pipelines to $PATH
export PATH="/gs1/RTS/OpenOmics/prod/rna-seek/latest:${PATH}"
export PATH="/gs1/RTS/OpenOmics/prod/metavirs/latest:${PATH}"
While, singularity is installed to the BigSky system and available upon login.
Outside NIH servers¶
Please follow the relevent instructions on the related package(s): Snakemake and singularity
Quickstart¶
After installing all the dependencies you then test the workflow functionality using a the dry run switch in the weave frontend.