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JDACS4C-IMPROVE / DrugCell

A visible neural network model for drug response prediction
MIT License
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DrugCell Build: 2023-09-13-02 - file not in path #30

Closed wilke closed 11 months ago

wilke commented 11 months ago 
          Build: 2023-09-13-02

Command: singularity exec --bind ${TEST_DIR}:/candle_data_dir build/DrugCell.sif train.sh 2 /candle_data_dir --epochs 1 Status: Failed Depends on:

Output: 

CMD = python /usr/local/DrugCell/train.py --epochs 1
COMMAND: python /usr/local/DrugCell/train.py --epochs 1
/usr/local/DrugCell
/usr/local/DrugCell/train.py
COMMAND: python /usr/local/DrugCell/train.py --epochs 1
using data from /candle_data_dir
/candle_data_dir//Data
python3: can't open file 'preprocessing_new.py': [Errno 2] No such file or directory
using original data placed in /candle_data_dir//Data
using CUDA_VISIBLE_DEVICES 1
using CANDLE_DATA_DIR /candle_data_dir
using CANDLE_CONFIG

Originally posted by @wilke in https://github.com/JDACS4C-IMPROVE/Singularity/issues/36#issuecomment-1718378484

wilke commented 11 months ago

Is in path:

singularity shell --bind `pwd`/tmp:/candle_data_dir build/DrugCell.sif train.sh 1 /candle_data_dir --epochs 1
Singularity> which train.sh
/usr/local/DrugCell/train.sh
Singularity> which train.py
/usr/local/DrugCell/train.py
Singularity> which preprocessing_new.py
/usr/local/DrugCell/preprocessing_new.py