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feat(executor): upgrade to Snakemake v8 (#103)
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Alputer committed Oct 29, 2024
1 parent b3e4727 commit 01d6c8b
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Showing 7 changed files with 337 additions and 190 deletions.
1 change: 1 addition & 0 deletions AUTHORS.md
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Expand Up @@ -3,6 +3,7 @@
The list of contributors in alphabetical order:

- [Agisilaos Kounelis](https://orcid.org/0000-0001-9312-3189)
- [Alp Tuna](https://orcid.org/0009-0001-1915-3993)
- [Audrius Mecionis](https://orcid.org/0000-0002-3759-1663)
- [Camila Diaz](https://orcid.org/0000-0001-5543-797X)
- [Giuseppe Steduto](https://orcid.org/0009-0002-1258-8553)
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24 changes: 19 additions & 5 deletions Dockerfile
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Expand Up @@ -89,22 +89,36 @@ RUN chmod +x /usr/local/bin/magick
# Are we debugging?
ARG DEBUG=0
# hadolint ignore=DL3013
RUN if [ "${DEBUG}" -gt 0 ]; then pip install --no-cache-dir -e ".[debug,xrootd]"; else pip install --no-cache-dir ".[xrootd]"; fi;
RUN if [ "${DEBUG}" -gt 0 ]; then pip install --no-cache-dir -e ".[debug]"; else pip install --no-cache-dir .; fi;

# Are we building with locally-checked-out shared modules?
# hadolint ignore=DL3008,DL3013
RUN apt-get update -y && \
apt-get install -y --no-install-recommends \
git && \
cmake \
g++ \
gcc \
git \
libssl-dev \
make \
python3.12-dev \
uuid-dev && \
if test -e modules/reana-commons; then \
if [ "${DEBUG}" -gt 0 ]; then \
pip install --no-cache-dir -e "modules/reana-commons[snakemake_reports]" --upgrade; \
pip install --no-cache-dir -e "modules/reana-commons[snakemake,snakemake-xrootd]" --upgrade; \
else \
pip install --no-cache-dir "modules/reana-commons[snakemake_reports]" --upgrade; \
pip install --no-cache-dir "modules/reana-commons[snakemake,snakemake-xrootd]" --upgrade; \
fi \
fi && \
apt-get remove -y \
git && \
cmake \
g++ \
gcc \
git \
libssl-dev \
make \
python3.12-dev \
uuid-dev && \
apt-get autoremove -y && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
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4 changes: 1 addition & 3 deletions reana_workflow_engine_snakemake/cli.py
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Expand Up @@ -20,7 +20,7 @@
from reana_commons.workflow_engine import create_workflow_engine_command

from reana_workflow_engine_snakemake.config import LOGGING_MODULE
from reana_workflow_engine_snakemake.executor import run_jobs
from reana_workflow_engine_snakemake.runner import run_jobs

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logging.basicConfig(level=REANA_LOG_LEVEL, format=REANA_LOG_FORMAT)
Expand Down Expand Up @@ -49,8 +49,6 @@ def run_snakemake_workflow_engine_adapter(
log.info(f"Workflow spec received: {workflow_file}")
publisher.publish_workflow_status(workflow_uuid, running_status)
success = run_jobs(
rjc_api_client,
publisher,
workflow_workspace,
workflow_file,
workflow_parameters,
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