Snakemake draft #41
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Snakemake draft #41
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Sorry, forgot to add instructions for testing: # install snakemake
mkdir working-dir
cd working-dir
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p conda-install
source conda-install/etc/profile.d/conda.sh
conda install mamba -c conda-forge --yes
mamba create -c bioconda -c conda-forge -n snakemake snakemake-minimal --yes
conda activate snakemake
# run workflow
git clone https://github.com/c-scale-community/use-case-hisea.git
cd use-case-hisea/
git checkout --track origin/snakemake
snakemake -c1 pre_processing_boundary --use-conda --conda-frontend mamba |
Closed
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Fixed now the snakemake rule for Note that I had to manually execute: |
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@backeb @lorincmeszaros I fixed the issue with I think the best next step is for us three to have a dedicated meeting to move this forward with new steps for the workflow (if you still want to go down the snakemake route) |
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I've forwarded the meeting for Friday morning, where Lőrinc and I are planning to work on this. |
backeb
reviewed
Dec 16, 2022
| #make the /data/tmp directory if it does not exist | ||
| Path('/data/cmems/tmp').mkdir(parents=True, exist_ok=True) | ||
| #make the data/tmp directory if it does not exist | ||
| Path('data/cmems/tmp').mkdir(parents=True, exist_ok=True) |
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@sebastian-luna-valero I think we change these it will affect running these scripts from docker...
backeb
approved these changes
Dec 16, 2022
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I was playing a bit with https://github.com/c-scale-community/c-scale-tutorial-snakemake
Then decided to create this draft for a snakemake workflow for HiSea.
Regarding #40, Snakemake can also help with job submission to SLURM:
https://snakemake.readthedocs.io/en/stable/executing/cluster.html