Docker without pandas - Githubissues

ssadedin / ximmer

Ximmer is a system for CNV calling on exome and targeted genomic sequencing

http://ssadedin.github.io/ximmer/

GNU Lesser General Public License v2.1

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Docker without pandas #19

Closed pixuenan closed 5 years ago

pixuenan commented 5 years ago

Hello,

When I run ximmer docker at the final stage to consolidate reports, I get this error

Ximmer  [1] INFO    |7:53:07 Executing python script ... 
Traceback (most recent call last):
  File "/usr/local/ximmer/src/main/python/cnv_size_histogram.py", line 2, in <module>
    import pandas as pd
ImportError: No module named pandas
Caught: java.lang.RuntimeException: Execution of python script /./.ximmertmp/4342302419878666-0/XimmerPythonScript.sh failed:

Seems the docker need pandas to run properly.

ssadedin commented 5 years ago

Thanks for mentioning this - I will try and reproduce and update the container. Not sure how I ran it successfully previously without pandas installed.

pixuenan commented 5 years ago

Hi Simon,

Thanks for your reply. Sorry for create this issue, after a close check with the build process of the docker image, I found the installation of pandas was failed. So my docker image was created "successfully" without pandas.