GCP Snakemake

Hey everyone,

I'm working on a project using snakemake in GCP VM, i have a problem that i want to remote output files to GCP buckets, but, i have an error like this.

> NoAuthHandlerFound in line 10 of /home/fadwa_elkhaddar8/GCP/snakefile:
No handler was ready to authenticate. 1 handlers were checked. ['HmacAuthV1Handler'] Check your credentials
  File "/home/fadwa_elkhaddar8/GCP/snakefile", line 10, in <module>
  File "/home/fadwa_elkhaddar8/miniconda3/envs/snakemake/lib/python3.6/site-packages/snakemake/remote/GS.py", line 13, in __init__
  File "/home/fadwa_elkhaddar8/miniconda3/envs/snakemake/lib/python3.6/site-packages/snakemake/remote/S3.py", line 35, in __init__
  File "/home/fadwa_elkhaddar8/miniconda3/envs/snakemake/lib/python3.6/site-packages/snakemake/remote/S3.py", line 146, in __init__
  File "/home/fadwa_elkhaddar8/miniconda3/envs/snakemake/lib/python3.6/site-packages/boto/__init__.py", line 141, in connect_s3
  File "/home/fadwa_elkhaddar8/miniconda3/envs/snakemake/lib/python3.6/site-packages/boto/s3/connection.py", line 194, in __init__
  File "/home/fadwa_elkhaddar8/miniconda3/envs/snakemake/lib/python3.6/site-packages/boto/connection.py", line 569, in __init__
  File "/home/fadwa_elkhaddar8/miniconda3/envs/snakemake/lib/python3.6/site-packages/boto/auth.py", line 1021, in get_auth_handler

Can you please help me how to resolve this problem

snakemake gcp

• 964 views • link

updated 2.5 years ago by GenoMax

• written 2.5 years ago by Fadwa •

Most of the log above seem to be referring to S3 which is AWS command line utils. You will need to use google CLI which minimally require python 3.8.

• 0 views • link

written 2.5 years ago by GenoMax

How can i do this ?! because i'm working on VM directly via Google Cloud console.

• 0 views • link

written 2.5 years ago by Fadwa •

You will need to provide details of what your snakefile looks like for others to help. Please verify that the SRA accessions you are downloading allow free egress (not all do) otherwise you will need to pay for the downloads.

• 0 views • link

written 2.5 years ago by GenoMax

0 answers

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