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f-heeger / two_marker_metabarcoding

Pipeline for metabarcoding of fungi with more than one marker (5.8S and ITS2)
GNU Lesser General Public License v3.0
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test run #5

Closed clemdawg closed 3 years ago

clemdawg commented 3 years ago

Hello Felix,

After the installation I tried: snakemake --use-conda -s metabarcoding.snakemake.py -j 2

I get the following error message Building DAG of jobs... Creating conda environment envs/multiqc.yaml... Downloading and installing remote packages. Environment for envs/multiqc.yaml created (location: .snakemake/conda/2a0756b32b9f6d2e127d146793de8ded) Creating conda environment envs/vsearch.yaml... Downloading and installing remote packages. Environment for envs/vsearch.yaml created (location: .snakemake/conda/742f1cbd61c45fbba553b1c74ecedf32) Creating conda environment envs/lambda.yaml... Downloading and installing remote packages. CreateCondaEnvironmentException: Could not create conda environment from /Users/home/fungi_pipe/two_marker_metabarcoding-master/envs/lambda.yaml: Collecting package metadata (repodata.json): ...working... done Solving environment: ...working... failed

ResolvePackageNotFound:

File "/Users/home/miniconda3/envs/snakemake/lib/python3.9/site-packages/snakemake/deployment/conda.py", line 387, in create

Any idea how I can resolve this?

f-heeger commented 3 years ago

This is most likely an issue with the lambda2 conda distribution not containing executables for MacOS. This could only be fixed by the maintainers of that package including them.

A possible workaround might be to install lambda manually and change the rules that use it to not use conda (or run those rules on their own without the use-conda flag).

clemdawg commented 3 years ago

Hi Felix,

sorry for not responding earlier.

Alice helped me fix the problem with the lamba2 installation.

The pipeline seems to work now.

Have a nice weekend.

Clemens

On 09.04.2021, at 10:26, Felix Heeger @.***> wrote:

This is most likely an issue with the lambda2 conda distribution not containing executables for MacOS. This could only be fixed by the maintainers of that package including them.

A possible workaround might be to install lambda manually and change the rules that use it to not use conda (or run those rules on their own without the use-conda flag).

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