Merge branch 'master' into develop

.gitlab-ci.yml

+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

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}"

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