Error when running example in gvanno about gvanno HOT 4 CLOSED

I am not sure what happens to the

"docker pull sigven/gvanno:1.4.1 (gvanno annotation engine)"
Which is a .sif file?

Where is this used in the above command?

regards,

Nandan

from gvanno.

Dear Nandan,

Thanks for reaching out. I think this is a Singularity issue, I am trying to see what's causing it. Just to check: Have you built the singularity image, following the instructions here:

https://github.com/sigven/gvanno#11-installation-of-singularity-optional

The singularity part is contributed by another user, but according to the code, it seems you should have a a gvanno.simg in your srcdirectory after installing Singularity for gvanno. Is that in place for you?

Tha above commend (docker pull.. ) is used when running the Docker workflow, should not be run in gvanno.py when using the Singularity version I believe.

kind regards,
Sigve

from gvanno.

Hi Nandan,
which version of singularity are you running on your computer?

It looks like singularity exec command executed inside gvanno.py cannot make sense of the -W option, so I am wondering if that option is available in your installation at all.

best,
tina

from gvanno.

Thanks Sigve and Tina for your responses.

I actually went ahead and used Docker to run gvanno and it ran seamlessly :-) on my local mac.

Thanks again,

Nandan

from gvanno.