If we just pip install the repo, the scripts, which are not python files, are not copied in the install folder and
batch process tile fails silently. Copying one of the sbatch command printed reveals the issue:
(iss-preprocess) [blota@int003 iss-preprocess]$ sbatch --parsable --export=DATAPATH=becalia_rabies_barseq/BRAC8501.6a/chamber_07,ROI=14,TILEX=7,TILEY=4 --output=/camp/home/blota/slurm_logs/iss_basecall_tile_14_7_4_%j.out /camp/home/blota/.conda/envs/iss-preprocess/lib/python3.10/site-packages/scripts/basecall_tile.sh
sbatch: error: Unable to open file /camp/home/blota/.conda/envs/iss-preprocess/lib/python3.10/site-packages/scripts/basecall_tile.sh
I don't see any trivial fix for now, so we can maybe just tell people to keep the -e flag
If we just
pip installthe repo, the scripts, which are not python files, are not copied in the install folder andbatch process tile fails silently. Copying one of the
sbatchcommand printed reveals the issue:I don't see any trivial fix for now, so we can maybe just tell people to keep the
-eflag