Download wf in CMD

[passelma42]

Ask away!

Hi, is it possible to download the wf through command line and run it offline? If so, how would I go about?

[julibeg]

Hi @passelma42! If you've run the wf to completion once (i.e. the pipeline and docker / singularity images have been pulled), you can run it without internet using the regular CLI command.

Please let us know if you're running into any issues.

[passelma42]

Hi Julian, Thanks. So I'll need to run it in the same working directory to where the singularity folder/images are pulled? Is it also possible to run it with apptainer? This would be our togo option for running containers on our HPC. Greets Pieter Verzonden vanaf Outlook voor Android<https://aka.ms/AAb9ysg>

…

________________________________ From: Julian Libiseller-Egger ***@***.***> Sent: Wednesday, December 20, 2023 9:51:34 PM To: epi2me-labs/wf-amplicon ***@***.***> Cc: Pieter Asselman ***@***.***>; Mention ***@***.***> Subject: Re: [epi2me-labs/wf-amplicon] Download wf in CMD (Issue #8) Hi @passelma42<https://github.com/passelma42>! If you've run the wf to completion once (i.e. the pipeline and docker / singularity images have been pulled), you can run it without internet using the regular CLI command. Please let us know if you're running into any issues. — Reply to this email directly, view it on GitHub<#8 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ARRQI22VVC26UCBL3LZUIHDYKNFVNAVCNFSM6AAAAABA446H4KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNRVGEZDEMRQGA>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[julibeg]

Hi Pieter and sorry for the delay!

So I'll need to run it in the same working directory to where the singularity folder/images are pulled?

You can set the env variable NXF_SINGULARITY_CACHEDIR to tell singularity where to put / look for images. Depending on your HPC environment, some additional setup for running singularity offline might be necessary.

Is it also possible to run it with apptainer?

Apptainer and Singularity can be used interchangeably. Depending on your Apptainer installation, you might need to create a symlink named singularity in a directory somewhere in your $PATH to make it available.

Good luck!