galaxyproject / galaxyproject/training-material

Docker container: Error during analysis task

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Description

Hi,
I was trying to execute the [Regression in Machine Learning hands-on](https://training.galaxyproject.org/training-material/topics/statistics/tutorials/regression_machinelearning/tutorial.html) by using the [docker container](https://quay.io/repository/galaxy/statistics-training).
After uploading data and setting parameters according to the hands-on instructions I run the analysis but after a while, I got this error:

```
Fatal error: Exit code 1 (Error occurred. Please check Tool Standard Error)
Using TensorFlow backend.
/export/tool_deps/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59/lib/python3.6/site-packages/sklearn/externals/joblib/__init__.py:15:
DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and
will be removed in 0.23. Please import this functionality directly from
joblib, which can be installed with: pip install joblib. If this warning
is raised when loading pickled models, you may need to re-serialize
those models with scikit-learn 0.21+.
warnings.warn(msg, category=DeprecationWarning)
Traceback (most recent call last):
File
"/export/galaxy-central/database/job_working_directory/000/2/tmp6OCskg",
line 11, in
from galaxy_ml.utils import load_model, get_X_y
File
"/export/tool_deps/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59/lib/python3.6/site-packages/galaxy_ml/utils.py",
line 15, in
import xgboost
File
"/export/tool_deps/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59/lib/python3.6/site-packages/xgboost/__init__.py",
line 11, in
from .core import DMatrix, Booster
File
"/export/tool_deps/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59/lib/python3.6/site-packages/xgboost/core.py",
line 136, in
_LIB = _load_lib()
File
"/export/tool_deps/_conda/envs/mulled-v1-26f90eb9c8055941081cb6eaef4d0dffb23aadd383641e5d6e58562e0bb08f59/lib/python3.6/site-packages/xgboost/core.py",
line 128, in _load_lib
lib.XGBGetLastError.restype = ctypes.c_char_p
UnboundLocalError: local variable 'lib' referenced before assignment
```
The same occurred trying to run the [classification example](https://training.galaxyproject.org/training-material/topics/statistics/tutorials/classification_machinelearning/tutorial.html).

Running the same examples on an external Galaxy instance (for example https://usegalaxy.eu/) everything works fine.

Do I need to do something special using the docker container or is it an issue of the docker image?
Thank you in advance
Giovanni

Contributor guide

Open the contributing guide

Research direction

Start with the Docker image linked in the issue and reproduce the Regression in Machine Learning and classification tutorials using their documented inputs and parameters. Inspect the reported xgboost import traceback and container tool dependencies; done means both analyses complete successfully in the Docker container without the exit-code error.

Written by the indexing model from the issue text.

Assessment

Tech stack
docker, python, scikit-learn, tensorflow
Domain
devops, machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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