diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml new file mode 100644 index 0000000000000000000000000000000000000000..24ae9088c7a5a99aa374d3960353d4c59366c834 --- /dev/null +++ b/.gitlab-ci.yml @@ -0,0 +1,10 @@ +build-package: + stage: deploy + image: python:3.6 + script: + - pip install twine build + - cd run_af2 + - python3 -m build + - TWINE_PASSWORD=${CI_JOB_TOKEN} TWINE_USERNAME=gitlab-ci-token python3 -m twine upload --repository-url https://git.scicore.unibas.ch/api/v4/projects/${CI_PROJECT_ID}/packages/pypi dist/* + only: + - tags diff --git a/run_af2/bin/run_singularity b/run_af2/bin/run_singularity index 178bc8938095ccb92e36712a56bf9b388f299e53..ea850ea033a7d6ad308255bf5e445b7cc2b0f674 100755 --- a/run_af2/bin/run_singularity +++ b/run_af2/bin/run_singularity @@ -22,6 +22,12 @@ shift OUTDIR=$1 shift -script_path="$(cd "$(dirname "$0")" && pwd)" -sbatch --job-name=af2 --workdir=$(pwd) --cpus-per-task=12 --mem=85G --qos=1week ${SLURM_AF_PARAMS} --wrap="module purge; module load Python/3.6.6-foss-2018b; python ${script_path}/run_singularity.py ${AF_PIPELINE_PARAM} ${OUTDIR} ${FASTAFILE}" +sbatch --job-name=af2 \ + --workdir=$(pwd) \ + --cpus-per-task=12 \ + --mem=85G \ + --qos=1week \ + --export=ALL \ + ${SLURM_AF_PARAMS} \ + --wrap="run-af2 ${AF_PIPELINE_PARAM} ${OUTDIR} ${FASTAFILE}" diff --git a/run_af2/setup.cfg b/run_af2/setup.cfg index 6b2c7da917b1f06989bc18454ba92de7ca4f1e51..ac561b3f32c2ef3f183b7edaad6cf8dc7826cda3 100644 --- a/run_af2/setup.cfg +++ b/run_af2/setup.cfg @@ -28,4 +28,4 @@ where = src [options.entry_points] console_scripts = - run_af2 = run_af2.run_singularity:main \ No newline at end of file + run-af2 = run_af2.run_singularity:main \ No newline at end of file