version 3.0.0 fails to create environments (stops at the RNAseq)

[sunta3iouxos]

the envs/shared.yaml and envs/createIndices.yaml are created without issues.
but the whole process just fails in the next level

Creating environment (3/24) from envs/rna_seq.yaml with hash 7b098b94bad80d0be19669458b1d7ef9
Channels:
 - conda-forge
 - bioconda
Platform: linux-64
Collecting package metadata (repodata.json): ...working... done
Solving environment: ...working... done
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... There was an error when creating the environments!

[WardDeb]

Is this something reproducible ? I.e. does re-running createEnvs keep resulting in the same behavior ?

[sunta3iouxos]

got it again today the same error. it stalls at the exucuting transaction and then I got the fail.

[katsikora]

Did you run snakePipes config --condaEnvDir and provide a path with sufficient storage? The default currently points to /tmp and I wonder if the disk space becomes an issue at some point?

[sunta3iouxos]

Did you run snakePipes config --condaEnvDir and provide a path with sufficient storage? The default currently points to /tmp and I wonder if the disk space becomes an issue at some point?

all environments are set up in /scratch, so that no restrictions will apply, I touch the folders monthly to not be wiped out and also taking backup of them in case they do.

$snakePipes info
------------------------- Info -------------------------

The global configuration file is:
    /scratch/tgeorgom/mamba/snakePipes/lib/python3.12/site-packages/snakePipes/shared/defaults.yaml
    --> tempDir in the global configuration = /scratch/tgeorgom/temp
    --> The snakemake profile used =  /scratch/tgeorgom/mamba/snakePipes/lib/python3.12/site-packages/snakePipes/shared/profiles/snakepipes_genericprofile

and defaults.yalm looks like:

condaEnvDir: /scratch/tgeorgom/mamba/snakePipes/env
configMode: manual
emailSender: null
max_thread: 100
oldConfig: null
onlySSL: false
organismsDir: shared/organisms
smtpPassword: null
smtpPort: 0
smtpServer: null
smtpUsername: null
snakemakeOptions: ''
#snakemakeProfile: shared/profiles/local
snakemakeProfile: shared/profiles/snakepipes_genericprofile
tempDir: /scratch/tgeorgom/temp
toolsVersion: true

those are the limits for /scratch

               +-------------------------------------------------------------------------------------------------------
                |                     Used: |            Soft Limit: |            Hard Limit: |            Grace Time: |
    Block Quota |                      26GB |                   30TB |                   40TB |                      - |
     File Quota |                   267,087 |              1,048,576 |              2,097,152 |                      - |
                +-------------------------------------------------------------------------------------------------------

[WardDeb]

If you try the --only flag to install other environments aside from the rna-seq one, do these get installed properly ?