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biobakery / biobakery_workflows

bioBakery workflows is a collection of workflows and tasks for executing common microbial community analyses using standardized, validated tools and parameters.
http://huttenhower.sph.harvard.edu/biobakery_workflows
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worflow issue using conda #33

Closed marcelladane closed 1 year ago

marcelladane commented 1 year ago

Hello, I have been trying to create an environment with biobakery workflows. When trying to use conda I get the following error:

conda create -n biobakery -c biobakery biobakery_workflows

Traceback (most recent call last):
      File "/home/bench-user/.apps/conda/lib/python3.10/site-packages/conda/gateways/repodata/__init__.py", line 161, in conda_http_errors
        yield
      File "/home/bench-user/.apps/conda/lib/python3.10/site-packages/conda/gateways/repodata/__init__.py", line 127, in repodata
        response.raise_for_status()
      File "/home/bench-user/.apps/conda/lib/python3.10/site-packages/requests/models.py", line 1021, in raise_for_status
        raise HTTPError(http_error_msg, response=self)
    requests.exceptions.HTTPError: 404 Client Error: Not Found for url: https://conda.anaconda.org/biobakery/linux-64/current_repodata.json

So I tried to install pip. But then the error is in the DB: Unable to find database KNEADDATA_DB_HUMAN_GENOME

I tried to run, without success KNEADDATA_DB_HUMAN_GENOME=/home/biobakery/biobakery_workflows/kneaddata_db_human_genome

Can I get help to get the pipeline setup please.

github-actions[bot] commented 1 year ago

Thank you for creating this issue. We currently field issues through our bioBakery Discourse Support Forum. If you would please post the issue to discourse we would be happy to sync up with you to get it resolved.