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Commit f51e1d68 authored by David Schäfer's avatar David Schäfer
Browse files

added Dockerfile

parent 142c9d40
FROM python:3.9
RUN git clone --recursive /pipeline
WORKDIR /pipeline
RUN cd saqc && git apply ../translator.patch && cd ..
RUN mkdir .cache
RUN pip install --no-cache-dir --upgrade pip
RUN pip install --no-cache-dir -r saqc/requirements.txt
RUN pip install --no-cache-dir -r requirements.txt
# CMD snakemake -j4 --forceall --printshellcmds --keep-going --restart-times 3
......@@ -6,9 +6,7 @@ Get a project overview here:
## Usage
Get and run the qc program:
Get and run pipeline
git clone --recursive
cd seefo
PYTHONPATH=saqc:$PYTHONPATH python --infile {data_in.parquet} --outfile {data_out.parquet} --configfile {configs/431.csv}
docker run --env-file /path/to/file.env --network host --rm snakemake -j2 --forceall --keep-going --restart-times 3
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