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mamba is difficult to install in grenepipe environment #40
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Hey @wangshuangyi, it seems that you first created the As for naming the environments: That is not something that snakemake uses. If you create all the individual tool environments manually, snakemake won't know about it, and won't use them, so that would not help you. Instead, get mamba to work as documented, install and activate the Hope that helps, so long |
Thank you very much for your reply. I have solved the problem of mamba, but as shown below, this command is often interrupted due to my network environment, may I ask whether I can re-run this command after the interruption? Also, I notice that when I run snakemake --use-conda --conda-frontend mamba --cores 4 --directory example/, each yaml will generate a different file after completion under path/grenepipe-0.12.2/example/.snakemake/conda/. If I execute a different project, do I need to run $snakemake --use-conda --conda-frontend mamba --cores 4 --directory xxx/? |
Hi @wangshuangyi,
Very good!
That is a more general conda/mamba question. If any install step fails, you might need to delete the env first again before re-trying (
Yes, for some reason, snakemake always installs the environments locally in the directory where you run your analysis (the one specified via
I'd recommend to read the whole wiki. That might answer most of your questions. If not, let me know. Cheers |
Dear @wangshuangyi, any update on this, or can be close the issue? Cheers |
Closing the issue now, but feel free to re-open if this is still and issue. |
(grenepipe) [sysu_mhwang_1@sy3ubuntu1804-23101937-698d4864d-99fwt envs]$conda install mamba
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): /
Software installation would be too slow without mamba.I noticed that the yaml files in the envs folder don't have names, can I write a name for each yaml file and then install each virtual environment separately in the mamba environment
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