adding gem_tools

[emikar]

Adding a suite of tools for interacting with and analyzing genome-scale metabolic models (GEMs). These modules are primarily based on the cobrapy package, with which I (the contributor) am not affiliated.

FOR CONTRIBUTOR:

• I have read the CONTRIBUTING.md document and this tool is appropriate for the tools-iuc repo.
• License permits unrestricted use (educational + commercial)
• This PR adds a new tool or tool collection
• This PR updates an existing tool or tool collection
• This PR does something else (explain below)

[bgruening]

Did you removed your .shed.yml file?

[emikar]

Very curious. The errors all indicate that the cobra module is missing, but when searching the conda channels suggested in the galaxyproject conda FAQ to be standard for Galaxy, it looks like cobra should be readily available. Am I overlooking something?

$ conda search cobra -c iuc -c conda-forge -c bioconda
Loading channels: done
# Name                       Version           Build  Channel             
cobra                        0.4.0b6          py27_0  bioconda            
cobra                        0.4.0b6          py34_0  bioconda            
cobra                        0.4.0b6          py35_0  bioconda            
cobra                          0.4.0          py27_0  bioconda            
cobra                          0.4.0          py27_1  bioconda            
cobra                          0.4.0          py34_0  bioconda            
cobra                          0.4.0          py35_0  bioconda            
cobra                          0.4.0          py35_1  bioconda            
cobra                          0.4.0          py36_0  bioconda            
cobra                          0.4.0          py36_1  bioconda            
cobra                         0.10.1          py27_0  bioconda            
cobra                         0.10.1          py35_0  bioconda            
cobra                         0.10.1          py36_0  bioconda            
cobra                         0.10.1            py_1  bioconda            
cobra                         0.15.4            py_0  bioconda            
cobra                         0.16.0            py_0  bioconda            
cobra                         0.17.0            py_0  bioconda            
cobra                         0.17.1            py_0  bioconda            
cobra                         0.18.1    pyh864c0ab_1  bioconda            
cobra                         0.18.1    pyh9f0ad1d_0  bioconda            
cobra                         0.19.0    pyh864c0ab_0  bioconda            
cobra                         0.20.0    pyh3252c3a_0  bioconda            
cobra                         0.21.0    pyh3252c3a_0  bioconda            
cobra                         0.21.0    pyh5e36f6f_1  bioconda            
cobra                         0.21.0    pyhd8ed1ab_0  conda-forge         
cobra                         0.22.0    pyhd8ed1ab_0  conda-forge         
cobra                         0.22.1    pyhd8ed1ab_0  conda-forge         
cobra                         0.22.1    pyhd8ed1ab_1  conda-forge         
cobra                         0.23.0    pyhd8ed1ab_0  conda-forge         
cobra                         0.24.0    pyhd8ed1ab_0  conda-forge         
cobra                         0.25.0    pyhd8ed1ab_1  conda-forge         
cobra                         0.26.0    pyhd8ed1ab_0  conda-forge         
cobra                         0.26.2    pyhd8ed1ab_0  conda-forge         
cobra                         0.26.3    pyhd8ed1ab_0  conda-forge         
cobra                         0.27.0    pyhd8ed1ab_0  conda-forge         
cobra                         0.28.0    pyhd8ed1ab_0  conda-forge         
cobra                         0.29.0    pyhd8ed1ab_0  conda-forge         
cobra                         0.29.1    pyhd8ed1ab_0  conda-forge         

[emikar]

Thanks for the valuable feedback on formatting! I think it's much easier to read now, even for myself, and probably a lot easier to maintain!

The core issue remains however, with the automatic tests failing. I don't have any such issues running the tests on my own machine using planemo test (see attached image). Are there any particular settings I need to run planemo test with to reproduce the particular merge test running here? Any help would be greatly appreciated :)

[bgruening]

I restarted the CI and its green now :)

[bgruening]

@emikar thanks a lot. Sorry for torturing you so long.

[emikar]

@emikar thanks a lot. Sorry for torturing you so long.

Haha, not at all! There was some excellent feedback, and I definitely learned a trick or three. Thanks for the patience! :)