Hi Spatial user, I try to use this pipeline by running a test run:

nextflow run nf-core/spatialvi \

-profile singularity,test *-r* dev

However, I got error related to render notebook quarto render I think. My I know the code that you run successful? Thank you so much!

I think this might be something with a weird interaction between Quarto and Singularity. Would you be able to run with Docker instead and test?

Hi Chris, From what I see, it looks like a temp folder issue actually: it tries to create a temporary file or directory, but fails with "NotFound: No such file or directory". Could you check what is in your TMPDIR environment variable and if you have write access on it?

echo $TMPDIR

You could also change it before running the pipeline, with:

export TMPDIR=/path/to/custom/tmp

(to a folder in your personal space for example)

Hi @Christophe Avenel I got this:

echo $TMPDIR

/scratch

I guess you don't have write permission on /scratch. Try my second command like:

mkdir /usr3/bustaff/chdoan/tmp
export TMPDIR=/usr3/bustaff/chdoan/tmp
echo $TMPDIR

Now I have:

echo $TMPDIR

/usr3/bustaff/chdoan/tmp

So I can try the pipeline again, right?

Yes I would do that. Just in case, you can also try to change TMPDIR for singularity with:

export SINGULARITY_TMPDIR=/usr3/bustaff/chdoan/tmp

and then run the pipeline

Hi @Christophe Avenel unfortunately, seem I have the same error. Thank you so much!

That's unfortunate. Maybe you could have a look here: https://keun-hong.github.io/bioinformatics/temp-files-nf-core/ where they tried to change the temp dir for singularity execution and ended up installing a different version of Singularity. Could be one thing to try...

Thanks @Christophe Avenel for your suggestion! I ran with SingularityCE 4.2.1 but still get the error 😅.

Did you also change the environment variables to a different tmp folder like discussed, in the terminal just before running the pipeline?

I updated singularity a few week ago

singularity-ce version 4.1.5-1.el8

and ran your code:

mkdir /usr3/bustaff/chdoan/tmp
export TMPDIR=/usr3/bustaff/chdoan/tmp
echo $TMPDIR
export SINGULARITY_TMPDIR=/usr3/bustaff/chdoan/tmp

Then submit my script with the pipeline. Hope that is the correct way.