Problem running about getorganelle HOT 5 CLOSED

Hi Eugene and Allison,

I just made the change which is making the index into the user assigned output directory. Let me know if you have any other suggestions!

Jianjun

from getorganelle.

Hi Allison,

You installed GetOrganelle in the root directory as I saw from log, it might be the permission issue. You should make the directory writable for Bowtie2 to output the index. You might also need to add sudo before chmod:

sudo chmod +w /GetOrganelle/Library/SeqReference

Please let me know the updates. Good luck!

Jianjun

from getorganelle.

Hi Jianjun

The way that you provide the library is not conducive to running this tool in a shared (cluster) environment nor through containers since.

We run bioinformatics tools in Singularity containers and I've solved Allison's issue by cloning the repo in her $HOME, followed by specifying the container of your tool (which I packaged) with the -s flag to her $HOME/GetOrganelle/Library.

I would suggest perhaps looking at ways of splitting the library out and allowing it to be pulled in at runtime per user to the user's directory? This would alleviate the issues with multiple users trying to run it at the same time or run it via containers.

Eugene

from getorganelle.

Hi Eugene,

Actually once bowtie2 index was made for the first time, the index could be shared and would not be overwritten any more in this version of GetOrganelle. I mean there would not be a problem for multiple users to access it simultaneously. However it is indeed not a good way to configure bioinformatics tools - writing stuff back to the bin directory even only for the first time. You are absolutely right at that point.
I had thought of making the index into the user assigned output directory because making the bowtie2 index is actually very fast and space-costless.
Thank you very much for the suggestion and thanks for helping Allison!

Jianjun

from getorganelle.

I will hopefully get around to testing this soon, but I think you can close this issue now. Thanks so much for the quick feedback!

from getorganelle.