Missing SpatialDE package in Docker container for ST_SPATIAL_DE process

[lealiaxiong]

Description of the bug

Running the nf-core/spatialtranscriptomics pipeline on an EC2 instance with files in S3. Encountered an error in NFCORE_SPATIALTRANSCRIPTOMICS:ST:ST_DOWNSTREAM:ST_SPATIAL_DE process:

ModuleNotFoundError: No module named 'SpatialDE'

Command used and terminal output

nextflow run \
    nf-core/spatialtranscriptomics \
    --input s3://<bucket_name>/s3_samplesheet.csv \
    --outdir s3://<bucket_name>/test_outputs/ \
    --spaceranger_reference s3://<bucket_name>/refdata-gex-mm10-2020-A.tar.gz \
    --spaceranger_probeset s3://<bucket_name>/Visium_Mouse_Transcriptome_Probe_Set_v1.0_mm10-2020-A.csv \
    -profile docker \
    -r dev \
    --max_memory 60.GB \
    --max_cpus 12


Output:
Apr-03 19:02:53.856 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 7; name: NFCORE_SPATIALTRANSCRIPTOMICS:ST:ST_DOWNSTREAM:ST_SPATIAL_DE (Visium_FFPE_Mouse_Brain); status: COMPLETED; exit: 1; error: -; workDir: /home/ec2-user/work/98/d4d2aae315f4018c786ee85f63d92a]
Apr-03 19:02:53.860 [Task monitor] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_SPATIALTRANSCRIPTOMICS:ST:ST_DOWNSTREAM:ST_SPATIAL_DE (Visium_FFPE_Mouse_Brain); work-dir=/home/ec2-user/work/98/d4d2aae315f4018c786ee85f63d92a
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_SPATIALTRANSCRIPTOMICS:ST:ST_DOWNSTREAM:ST_SPATIAL_DE (Visium_FFPE_Mouse_Brain)` terminated with an error exit status (1)
Apr-03 19:02:53.881 [Task monitor] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_SPATIALTRANSCRIPTOMICS:ST:ST_DOWNSTREAM:ST_SPATIAL_DE (Visium_FFPE_Mouse_Brain)'

Caused by:
  Process `NFCORE_SPATIALTRANSCRIPTOMICS:ST:ST_DOWNSTREAM:ST_SPATIAL_DE (Visium_FFPE_Mouse_Brain)` terminated with an error exit status (1)

Command executed:

  quarto render st_spatial_de.qmd         -P input_adata_processed:st_adata_processed.h5ad         -P n_top_spatial_degs:14         -P output_spatial_degs:st_spatial_de.csv
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_SPATIALTRANSCRIPTOMICS:ST:ST_DOWNSTREAM:ST_SPATIAL_DE":
      quarto: $(quarto -v)
      leidenalg: $(python -c "import leidenalg; print(leidenalg.version)")
      scanpy: $(python -c "import scanpy; print(scanpy.__version__)")
      SpatialDE: $(python -c "from importlib.metadata import version; print(version('SpatialDE'))")
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  
  Starting python3 kernel.../opt/conda/lib/python3.10/site-packages/IPython/paths.py:69: UserWarning: IPython parent '/' is not a writable location, using a temp directory.
    warn("IPython parent '{0}' is not a writable location,"
  /opt/conda/lib/python3.10/site-packages/IPython/paths.py:69: UserWarning: IPython parent '/' is not a writable location, using a temp directory.
    warn("IPython parent '{0}' is not a writable location,"
  Done
  
  Executing 'st_spatial_de.ipynb'
    Cell 1/9...Done
    Cell 2/9...Done
    Cell 3/9...
  
  An error occurred while executing the following cell:
  ------------------
  import scanpy as sc
  import pandas as pd
  import SpatialDE
  from matplotlib import pyplot as plt
  ------------------
  
  
  ---------------------------------------------------------------------------
  ModuleNotFoundError                       Traceback (most recent call last)
  Cell In[3], line 3
        1 import scanpy as sc
        2 import pandas as pd
  ----> 3 import SpatialDE
        4 from matplotlib import pyplot as plt
  
  ModuleNotFoundError: No module named 'SpatialDE'

Work dir:
  /home/ec2-user/work/98/d4d2aae315f4018c786ee85f63d92a

Tip: view the complete command output by changing to the process work dir and entering the command `cat .command.out`

Relevant files

No response

System information

AWS EC2 instance type: m7i-flex.4xlarge
AMI (OS): Amazon Linux 2023
Executor: local on EC2 instance
nf-core/spatialtranscriptomics version: dev

[fasterius]

Thanks for adding an issue! This error is due to the development-status of the pipeline, but will be fixed quite soon: PR #67. Sorry for any inconvenience this causes you.

[lealiaxiong]

Thanks! Not a big problem for me at this moment, just wanted to report in case it was unexpected.

[fasterius]

The #67 PR is now closed, so the issue should be fixed.