Update docker container with new Dockerfile

[toddcreasy]

Hi,

The last PR merges have created and made changes to the Dockerfile. I need to build the container from the Dockerfile we added to replace the “proteomics/cosmo:latest” container to include the new updates. Can someone take care of this for me?

Thanks,

-todd

[zhiaos]

Hi,

The image has been rebuilt with new tag "bzhanglab/cosmo:lastest"

Zhiao

[toddcreasy]

Thanks for doing this so quickly. Unfortunately, it looks like changes to the Dockerfile might have introduced an error (see below). Do you think this is related?

`Error executing process > 'METHOD2'

Caused by: Essential container in task exited

Command executed:

method2_function.py \ -d1 test_rna.tsv \ -d2 test_pro.tsv \ -s test_cli.tsv \ -l gender,msi \ -o method2_out

Command exit status: 1

Command output: Processing file: test_rna.tsv and test_pro.tsv

Command error: Processing file: test_rna.tsv and test_pro.tsv Traceback (most recent call last): File "//nextflow-bin/method2_function.py", line 255, in main() File "//nextflow-bin/method2_function.py", line 252, in main run(d1_file=d1_file, d2_file=d2_file, sample_file=sample_file, sample_labels=sample_label, out_dir=out_dir) File "//nextflow-bin/method2_function.py", line 117, in run upper = corr_matrix.where(np.triu(np.ones(corr_matrix.shape), k=1).astype(np.bool)) File "/usr/local/lib/python3.8/dist-packages/numpy/init.py", line 284, in getattr raise AttributeError("module {!r} has no attribute " AttributeError: module 'numpy' has no attribute 'bool' `

[zhiaos]

It's related to the newer numpy version in the docker image. I've updated the code. Please try again.

[toddcreasy]

@zhiaos - Sorry but I ran into another error. Any ideas on this one?

Error executing process > 'METHOD2'

Caused by: Essential container in task exited

Command executed:

method2_function.py \ -d1 test_pro.tsv \ -d2 test_rna.tsv \ -s test_cli.tsv \ -l gender,msi \ -o method2_out

Command exit status: 1

Command output: Processing file: test_pro.tsv and test_rna.tsv

Command error: Processing file: test_pro.tsv and test_rna.tsv Traceback (most recent call last): File "//nextflow-bin/method2_function.py", line 255, in main() File "//nextflow-bin/method2_function.py", line 252, in main run(d1_file=d1_file, d2_file=d2_file, sample_file=sample_file, sample_labels=sample_label, out_dir=out_dir) File "//nextflow-bin/method2_function.py", line 132, in run ('feature_selection', GenericUnivariateSelect(f_classif, 'fdr', param=0.1)), TypeError: init() takes from 1 to 2 positional arguments but 3 positional arguments (and 1 keyword-only argument) were given

[zhiaos]

looks like there are some changes in the latest version of sklearn for GenericUnivariateSelect. I've updated the code. Please try again.

[toddcreasy]

I forked the repo and did some more testing and I think the only thing that needs to be added to the Dockerfile is installing the docopt R package. Can you update that and then rebuild the image?

[zhiaos]

I think docopt is already available from the base image.

[toddcreasy]

Yes, you're right. Sorry about that! Thanks for all your help. Closing this.