Remote usage

[DeanTM]

Hi,

I'm trying to find a way to use the GUI remotely, but I can't figure out how to get the GUI to find data on the remote computer.

My data is on my remote computer, "my-remote". I find that I'm able to ssh into my-remote and then start OptiNiSt there with docker. I can then port forward the OptiNiSt port 8000 to my local computer with ssh -fN -L 8000:127.0.0.1:8000 user@my-remote. From here I can open the OptiNiSt on my local computer.

However, when I try to "load" data, the data nodes only allow me to upload data from my local computer, despite the fact that OptiNiSt is running remotely. Is there a way to allow OptiNiSt to look for my data on my-remote?

I have tried copying .tif files to the default /tmp/optinist/input (docs here) hoping that this would enable the image data node to find the files with "select image", but it doesn't work. Perhaps files need to be loaded before OptiNiSt is able to search this default directory?

How can I enable OptiNiSt to search for files remotely?

I realise that I should be able to create the computation graph in the GUI, then download the snakemake .yml file and run it from the command line, but in doing this I don't think I can inspect intermediate results as I build the graph.

Thank you!

[ykyamane]

Hi!

I have tried copying .tif files to the default /tmp/optinist/input....
In the case of docker version, you need to copy your file to the /tmp/optinist/input in the file system in the docker container. I think this should work for your case. Please try.

Best,
Yukako

[DeanTM]

Thank you for your response.

I tried that now, using docker cp to copy the files to /tmp/optinist/input in the container. I then confirmed that the files were there by copying them back, and they were.

But still the file is not available to "select image". I confirmed that optinist was running correctly by rerunning it with the sample2.tiff uploaded from my local computer.

I tried copying the file with both .tif and .tiff extensions, as below:

dean:input$ docker cp example.tiff [container_id]:/tmp/optinist/input
Successfully copied 265kB to [container_id]:/tmp/optinist/input
dean:input$ docker cp example.tiff [container_id]:/tmp/optinist/input/example.tif
Successfully copied 265kB to [container_id]:/tmp/optinist/input/example.tif

then checked that the the files were there by copying them back:

dean:input$ docker cp [container_id]:/tmp/optinist/input ./input_copies/
Successfully copied 73.8MB to /tmp/optinist/input/input_copies/
dean:input$ ls input_copies/
example.tif   memmap__d1_60_d2_60_d3_1_order_C_frames_2000_.mmap  sample2._rig__d1_60_d2_60_d3_1_order_F_frames_2000_.mmap
example.tiff  sample2                                             sample2.tiff

The files are there, but only sample2.tiff is available to be loaded:

I would appreciate any further advice. Thank you!

[ykyamane]

Hi Dean,

You need to reload the browser after copying your files to /tmp/optinist/input.
Please try if you haven't.

Another think you may want to try is to mount your data directory to the Docker container.