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metagenome-atlas / atlas

ATLAS - Three commands to start analyzing your metagenome data
https://metagenome-atlas.github.io/
BSD 3-Clause "New" or "Revised" License
377 stars 98 forks source link

Connda connection errors #587

Closed SilasK closed 1 year ago

SilasK commented 1 year ago

I and others encountered problems with conda trying to install wrappers. in atlas v3.12 and 3.13. using wrappers is the recommended way by snakemake but apparently it doesn't wark as expected.

SilasK commented 1 year ago

You got an error that looks something like 

Failed to open source file https://github.com/snakemake/snakemake-wrappers/raw/v1.19.0/bio/minimap2/aligner/environment.yaml
ConnectionError: HTTPSConnectionPool(host='github.com', port=443): Max retries exceeded with url: /snakemake/snakemake-wrappers/raw/v1.19.0/bio/minimap2/aligner/environment.yaml (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x2b589c337190>: Failed to establish a new connection: [Errno 101] Network is unreachable')), attempt 1/3 failed - retrying in 3 seconds...
SilasK commented 1 year ago

My solution was to download the wrapper repository, and then to run it from there.

git clone https://github.com/snakemake/snakemake-wrappers
atlas run --wrapper-prefix 'git+file://path/to/your/local/clone'
github-actions[bot] commented 1 year ago

There was no activity since some time. I hope your issue is solved in the mean time. This issue will automatically close soon if no further activity occurs.

Thank you for your contributions.

github-actions[bot] commented 1 year ago

There was no activity since some time. I hope your issue is solved in the mean time. This issue will automatically close soon if no further activity occurs.

Thank you for your contributions.