Request for Support: Galaxy Integration of mOTUs Tool

[ber58]

Hello,

I'm currently working on my Bachelor's project, where I'm developing a Galaxy wrapper for the mOTUs tool to seamlessly integrate it into the Galaxy Framework. This integration would make the tool more accessible and user-friendly, providing substantial benefits to users. We're enthusiastic about this addition, as it amplifies the capabilities of the Galaxy platform, opening up more opportunities for users.

For a successful testing phase of the Galaxy integration, I need a small test functional database and a dataset, each preferably under 1 MB in size.

If possible, could you please provide me with the necessary test functional database and dataset? Your help with this would be greatly appreciated as I move forward with the integration.

Thank you for your time and consideration.

Best regards,

Albert

[hjruscheweyh]

Dear @Alby-Git

Thank you for using mOTUs!

We have a test dataset but no test database. Using the test dataset on the standard database will finish within 10-20 seconds. I hope that this is ok for you.

Best,
test1_single.fastq.gz

Hans

[ber58]

Dear @hjruscheweyh,

Thank you for your prompt response and the test dataset. However, for our Galaxy integration, we also require a test database. It doesn't need to yield meaningful results but is essential for integration and testing. Could you assist us with this, or provide guidance on creating such a database?

Thank you for your support!

Best regards,

Albert

[hjruscheweyh]

Dear @Alby-Git

It is currently, due to a complex database format, not possible to simply subset the database for testing purposes. We are, however, actively developing a new database format for which we can then provide both, a complete database and a minimal testing database. My guess is that it should be ready for release by Mar/Apr 2023. I hope that that is not too late for you.

Best,
Hans

[ber58]

Dear Hans,

Thank you for your update on the database development. I appreciate the effort and understand the challenges involved in creating a new format.

Unfortunately, our project faces a tight deadline, making it difficult to wait until March or April 2023 for the implementation. We'll look for temporary alternatives, but we're keen to integrate your solution once it's available.

Thanks again for your hard work on this. Looking forward to the new database format.

Best,
Albert

[paulzierep]

why was this closed @Alby-Git ? Is there a test DB available ?

[ber58]

Dear @hjruscheweyh,

I wanted to follow up on our previous discussion regarding the database development. Have there been any updates or progress since we last communicated?

Thank you for your attention to this matter.

Best regards,
Albert

[paulzierep]

Dear @hjruscheweyh ,
I wanted to ask again if there is any way you could help us to create a smaller version of the reference DB. For context, in order to create Galaxy wrappers for a tool it is necessary to have test cases and these need to run on a github CI. Creating these tests with the large reference DB produces quiet some overhead for us. The DB we would need, does not have to produce biologically logic output, it only needs to be able to test that the tool actually works. Having a quick look on your DB, it seems that in only contains csvs, fatsa and some bowtie indices. Would it not be possible, to subsample DB using i.e. only one genome with its marker genes, or something like that ? If we can help in any way, please let us know.
Best regards,
Paul

[hjruscheweyh]

Dear @paulzierep @Alby-Git
Sorry for the late answer. We're still working towards a new mOTUs database (-format) for which it will be easy to release a tiny (<5MB) test database which should help the galaxy wrappers. I will keep you posted on the development on our side.

Best,
Hans