Cannot run SalmonTE in Snakemake pipeline

[ftabaro]

Hello,

I get an error about locking the results dir when running SalmonTE in Snakemake pipeline. I forked the repo and got it to run by disabling SalmonTE directory locking. Should I submit a pull request?

[hyunhwan-jeong]

@ftabaro,

Can you provide more details about the error to clarify what the exact issue is?

You can also send a pull request if you figured out how to resolve it.

Thank you,

Hyun-Hwan Jeong

[ftabaro]

Sure!

So, SalmonTE runs a Snakemake process after starting up. Snakemake creates lock files in the working directory it is running. This is to prevent other Snakemake processes to mess with the input/output files of the first process. In my use case, this feature prevents me to wrap SalmonTE in another Snakemake layer. To disable the locking mechanism, one can pass a command line parameter (--nolock), and that's what I did in my fork.

Now, I am not sure this behavior is desired and I am open for discussion. If you have other suggestions how to use SalmonTE in a Snakemake pipeline, I would be glad to hear.

[hyunhwan-jeong]

@ftabaro, I want to make sure I understand it correctly, do you mean running SalmonTE disrupt other snakemake runs, even the other runs do not touch any files that are locked by SalmonTE?

Hyun-Hwan Jeong

[ftabaro]

The other way. SalmonTE fails to start because it finds the lock of the outer pipeline.

[hyunhwan-jeong]

Got it, but I don't think a file being touched by multiple snakemakes simultaneously would be necessary and safe. Other thoughts?

Thank you,

Hyun-Hwan Jeong

[ftabaro]

One option could be to support Snakemake's --unlock option from SalmonTE top level scripts: e.g. salmonTE quant [...] --no-lock