snakemake-debugging.sh
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| # This is a small script (that typically I copy paste) on a Google Cloud instance | |
| # to set up an environment to mimic a worker. It includes installing snakemake, | |
| # retrieving a package with the working directory (which typically has the | |
| # version of snakemake I aim to develop or debug, and then interactively debugging | |
| # or doing this. | |
| sudo apt-get install -y wget bzip2 ca-certificates gnupg2 git | |
| wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh | |
| sudo chown -R $USER /opt | |
| bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda | |
| export PATH=$PATH:/opt/conda/bin | |
| conda install -y -c conda-forge mamba | |
| mamba create -q -y -c conda-forge -c bioconda -n snakemake snakemake snakemake-minimal --only-deps | |
| conda clean --all -y | |
| source activate snakemake | |
| mkdir -p /workdir | |
| sudo chown -R $USER /workdir | |
| cd /workdir | |
| wget -O gls.py https://raw.githubusercontent.com/snakemake/snakemake/master/snakemake/executors/google_lifesciences_helper.py | |
| chmod +x gls.py | |
| # This command needs to be updated with your download archive, there should be an install of snakemake inside | |
| python gls.py download snakemake-testing source/cache/workdir-09bda6e42f79362fe639d893de13495a84c2e2884961a9d828f9f865f33347f5.tar.gz /tmp/workdir.tar.gz | |
| tar -xzvf /tmp/workdir.tar.gz | |
| # Use -e to ensure we install from local directory | |
| pip install -e .[reports,messaging,google-cloud] | |
| pip install ipython | |
| echo"source activate snakemake">~/.bashrc | |
| export PATH=/opt/conda/envs/snakemake/bin:${PATH} | |
| # Your custom command will go here, add ipython / other interaction | |
| # into codebase before running! | |
| snakemake snakemake-testing/dirtest/testdir --snakefile Snakefile --force -j --keep-target-files --keep-remote --latency-wait 5 --scheduler greedy --attempt 1 --force-use-threads --max-inventory-time 0 --allowed-rules directory --nocolor --notemp --no-hooks --nolock --default-remote-provider GS --default-remote-prefix snakemake-testing/dirtest |