Snakemake Cloud execution command parameters (GCP)

1/3/2021

I want to use Snakemake on Google Cloud platform, so i used this tutorial : https://snakemake.readthedocs.io/en/stable/executing/cloud.html

I did the first steps, then I need to do this : https://snakemake.readthedocs.io/en/v5.8.0/executing/cluster-cloud.html#executing-a-snakemake-workflow-via-kubernetes

After reading the text below, i created a bucket named mybucketname in a project in my GCP account, and my command is :

snakemake --kubernetes --use-conda --default-remote-provider GS --default-remote-prefix mybucketname

The problem is that I get the error "Error : no Snakefile found, tried Snakefile, snakefile, workflow/Snakefile, workflow/snakefile."

I tried to change the name of the bucket in my command with another bucket name that doesn't exist, and i get the same error; which means the command doesn't find my bucket in GCP.

I haven't speficied a project name in the console (where my bucket is), so maybe it's the solution ? But i don't know how to specify it.

I have also tried to replace mybucketname with the Link URL and Link for gsutil parameters written in my bucket configuration, but it doesn't work

Can anyone help me ? Thanks

-- Bubsy
bucket
google-cloud-platform
kubernetes
python
snakemake

0 Answers