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nf-core / scdownstream

A single cell transcriptomics pipeline for QC, integration and making the data presentable
https://nf-co.re/scdownstream
MIT License
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MPLCONFIGDIR expected in $HOME outside what singularity allows #49

Closed smoe closed 4 days ago

smoe commented 4 days ago

Description of the bug

My home directory is not where the data is located and under -profile singularity the matplotlib config directory is then not available.

I then prefixed the invocation of nextflow with

MPLCONFIGDIR=$(pwd)

but that did not change the error.

Command used and terminal output

$ MPLCONFIGDIR=$(pwd) nextflow run nf-core/scdownstream -profile singularity --input samplesheet.csv --outdir results_20240701 -r dev

-[nf-core/scdownstream] Pipeline completed with errors-
Pulling Singularity image https://depot.galaxyproject.org/singularity/multiqc:1.22.2--pyhdfd78af_0 [cache /data/sm718/singularityCacheDir/depot.galaxyproject.org-singularity-multiqc-1.22.2--pyhdfd7
8af_0.img]
ERROR ~ Error executing process > 'NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:ADATA_UNIFY (JM_24h)'

Caused by:
  Process `NFCORE_SCDOWNSTREAM:SCDOWNSTREAM:PREPROCESS:ADATA_UNIFY (JM_24h)` terminated with an error exit status (1)

Command executed [/home/sm718/.nextflow/assets/nf-core/scdownstream/./workflows/../subworkflows/local/../../modules/local/adata/unify/templates/unify.py]:

  #!/usr/bin/env python3

  import scanpy as sc
  import scipy
  from scipy.sparse import csr_matrix
  import platform
....
Command error:
  Matplotlib created a temporary cache directory at /tmp/matplotlib-p_bjbrvd because the default path (/home/me/.config/matplotlib) is not a writable directory; it is highly recommended to set t
he MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
  Traceback (most recent call last):
    File ".command.sh", line 3, in <module>
      import scanpy as sc
    File "/opt/conda/lib/python3.12/site-packages/scanpy/__init__.py", line 45, in <module>
      from . import datasets, experimental, external, get, logging, metrics, queries
    File "/opt/conda/lib/python3.12/site-packages/scanpy/experimental/__init__.py", line 3, in <module>
      from . import pp
    File "/opt/conda/lib/python3.12/site-packages/scanpy/experimental/pp/__init__.py", line 3, in <module>
      from scanpy.experimental.pp._highly_variable_genes import highly_variable_genes
    File "/opt/conda/lib/python3.12/site-packages/scanpy/experimental/pp/_highly_variable_genes.py", line 26, in <module>
      from scanpy.preprocessing._distributed import materialize_as_ndarray
    File "/opt/conda/lib/python3.12/site-packages/scanpy/preprocessing/__init__.py", line 5, in <module>
      from ._deprecated.highly_variable_genes import filter_genes_dispersion
    File "/opt/conda/lib/python3.12/site-packages/scanpy/preprocessing/_deprecated/highly_variable_genes.py", line 13, in <module>
      from .._utils import _get_mean_var
    File "/opt/conda/lib/python3.12/site-packages/scanpy/preprocessing/_utils.py", line 78, in <module>
      @numba.njit(cache=True)
       ^^^^^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.12/site-packages/numba/core/decorators.py", line 229, in wrapper
      disp.enable_caching()
    File "/opt/conda/lib/python3.12/site-packages/numba/core/dispatcher.py", line 856, in enable_caching
      self._cache = FunctionCache(self.py_func)
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.12/site-packages/numba/core/caching.py", line 601, in __init__
      self._impl = self._impl_class(py_func)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^
    File "/opt/conda/lib/python3.12/site-packages/numba/core/caching.py", line 337, in __init__
      raise RuntimeError("cannot cache function %r: no locator available "
  RuntimeError: cannot cache function 'sparse_mean_var_minor_axis': no locator available for file '/opt/conda/lib/python3.12/site-packages/scanpy/preprocessing/_utils.py'


### Relevant files

_No response_

### System information

      N E X T F L O W
      version 24.04.2 build 5914
      created 29-05-2024 06:19 UTC (08:19 CEST)
      cite doi:10.1038/nbt.3820
      http://nextflow.io
Version of nf-core/scdownstream is current /dev
CentOS Linux
slurm
nictru commented 4 days ago

Could you please try the following:

  1. Create a file nextflow.config in your launch directory
  2. Add the following line: singularity.runOptions = '--no-mount tmp --writable-tmpfs'
  3. Try again

If this works, I can add it to the pipeline configuration

smoe commented 4 days ago

Yes, this works! Thank you tons!