search

maxplanck-ie / snakepipes

Customizable workflows based on snakemake and python for the analysis of NGS data
http://snakepipes.readthedocs.io
381 stars 85 forks source link

Error in CreateEnvs #799

Closed Leif78 closed 2 years ago

Leif78 commented 2 years ago

Dear all, I try to set up snakePipes on a newly installed ubuntu 18.04 and ubuntu 20.04. With both Ubuntus, Creating Environmnets halt in the middle of the set up and do not finnish. I paste in the log. Do anyone has any idea what to do?

(snakePipes) leif@leif-OptiPlex-9020:~/Desktop$ snakePipes createEnvs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/shared.yaml in /home/leif/miniconda3/envs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/createIndices.yaml in /home/leif/miniconda3/envs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/rna_seq.yaml in /home/leif/miniconda3/envs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/rMats.yaml in /home/leif/miniconda3/envs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/sc_rna_seq.yaml in /home/leif/miniconda3/envs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/sc_rna_seq_seurat3.yaml in /home/leif/miniconda3/envs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/sc_rna_seq_loompy.yaml in /home/leif/miniconda3/envs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/sc_rna_seq_alevinqc.yaml in /home/leif/miniconda3/envs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/sc_rna_seq_eisaR.yaml in /home/leif/miniconda3/envs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/dna_mapping.yaml in /home/leif/miniconda3/envs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/chip_seq.yaml in /home/leif/miniconda3/envs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/atac_seq.yaml in /home/leif/miniconda3/envs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/hic.yaml in /home/leif/miniconda3/envs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/wgbs.yaml in /home/leif/miniconda3/envs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/rmarkdown.yaml in /home/leif/miniconda3/envs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/preprocessing.yaml in /home/leif/miniconda3/envs Creating environment from /home/leif/miniconda3/envs/snakePipes/lib/python3.9/site-packages/snakePipes/shared/rules/envs/noncoding.yaml in /home/leif/miniconda3/envs Collecting package metadata (repodata.json): done Solving environment:

Thanks for help

LeilyR commented 2 years ago

how did you install the snakepipes and which version?

Leif78 commented 2 years ago

I did as described here, version 2.4.3: https://snakepipes.readthedocs.io/en/latest/content/setting_up.html

LeilyR commented 2 years ago

please try our latest version 2.5.2 on a fresh env

adRn-s commented 2 years ago

I am able to reproduce this using 2.4.3, my command is unable to solve the environment for noncoding.yaml too. This might be an infinite recursive 'bug' from upstream (conda).

@Leif78 : please let us know if you had any issues with the latest version, 2.5.2.

Leif78 commented 2 years ago

Hi, I installed 2.5.2, and the createEnvs has now runned in 21h without finishing.

Leif78 commented 2 years ago

Thanks for answers. CreateEnvs on version 2.5.2 is not working. It can not solve environment for noncoding.yaml as described before.

adRn-s commented 2 years ago

Please try with the new version, 2.5.3

Leif78 commented 2 years ago

createEnvs now works. Thanks for help!