search

galaxycomputationalchemistry / galaxy-tools-compchem

:mega: Galaxy Tools for Computational Chemistry
Apache License 2.0
14 stars 16 forks source link

Missing tool: gmx check #151

Closed Agnes-Petit closed 2 years ago

Agnes-Petit commented 2 years ago

Hello, In my job, I need the gmx check tool from GROMACS on Galaxy. I saw that it is currently not available. Have you started or plan to adapt it to Galaxy? If the answer is no, I would like to adapt it.

simonbray commented 2 years ago

@Agnes-Petit that would be great! Do you have some experience with Galaxy tool development? If not, there is a good tutorial here: https://planemo.readthedocs.io/en/latest/writing_standalone.html

Please let me know if you need any help.

Best wishes,

Simon

Agnes-Petit commented 2 years ago

I started developing tools in Galaxy recently. Thanks for the tutorial and for your help, Agnès

Agnes-Petit commented 2 years ago

In order to test an option of the tool, I need two .tpr files, however there is only one tpr file available in the test-data. Not knowing how the other files in this folder were obtained, I can't produce a second .tpr file from these files. Could you give me the name of the protein from which these files were obtained?

simonbray commented 2 years ago

Hi @Agnes-Petit, it is not an entire protein. but a five-residue peptide, in order to save space and compute resources. The peptide structure is in str_ions.gro. If it helps you can also use gmx editconf -f test-data/npt.tpr -o peptide.pdb to generate a PDB file.

Agnes-Petit commented 2 years ago

Hi, the gmx check script is ready however after discussion with my team, it appears that we want to include the team name in the owner of the .shed.yml. So we decided to publish the tool in the IUC directory. However if you have another solution to make the name of my team in the owner, we remain open to any suggestion.

simonbray commented 2 years ago

Hi @Agnes-Petit, the only reason for the 'owner' attribute in the .shed.yml file is to specify the user on the toolshed (app store for Galaxy tools). All the tools on this repo are uploaded by 'chemteam' as part of continuous integration when the PR is merged, which is the recommended way to create Galaxy tools. You can see also that on IUC all the .shed.yml files specify owner: iuc.

We don't want to claim ownership of any tool, we want to create a community that anyone can contribute to. :)

You can add yourself and team members to the maintainers section here if that helps? https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/blob/master/tools/gromacs/.shed.yml#L18

Agnes-Petit commented 2 years ago

Hi @simonbray, this solution suits us. I make the pull request.

simonbray commented 2 years ago

Added in #157