[BUG] Error creating conda environment

[allyhawkins]

Describe the bug
A clear and concise description of what the bug is.
If you have an error message or report that you can include, please do!

A user was running scpca-nf and everything ran successfully until they reached the export_anndata process. Here it appears that the workflow is trying to set up the conda environment for Zellkonverter, but can't. I do think part of this may be permissions.

To reproduce
If possible, please provide example code to reproduce the problem, including any information about the dataset where the problem occurred, if possible.

What command did you use to invoke the scpca-nf workflow?

What type of system are you using to run the workflow (local, slurm, AWS, etc.)?
If you are using a custom profile or config file, please include the file and settings you used.
Azure node

Version information
What version of scpca-nf are you using, and what version of Nextflow?
scpca-nf 0.5.2

Additional context
Add any other context about the problem here.

ERROR ~ Error executing process > 'sce_to_anndata:export_anndata (SCPCL000980)'

 

Caused by:

  Process `sce_to_anndata:export_anndata (SCPCL000980)` terminated with an error exit status (1)

 

Command executed:

 

  sce_to_anndata.R         --input_sce_file SCPCL000980_filtered.rds         --output_rna_h5 SCPCL000980_filtered_rna.hdf5         --output_feature_h5 SCPCL000980_filtered_null.hdf5

 

Command exit status:

  1

 

Command output:

  Collecting package metadata (current_repodata.json): ...working... done

  Solving environment: ...working... failed with repodata from current_repodata.json, will retry with next repodata source.

  Collecting package metadata (repodata.json): ...working... failed
 
Command error:
                            2/0/bin:/shared/home/ipushel/.cache/R/basilisk/1.10.2/0/bin:/shared/ho
                            me/ipushel/.cache/R/basilisk/1.10.2/0/condabin:/usr/local/sbin:/usr/lo
                            cal/bin:/usr/sbin:/usr/bin:/sbin:/bin:/mnt/scratch/assets/AlexsLemonad
                            e/scpca-nf/bin
           PYTHONNOUSERSITE=1
         REQUESTS_CA_BUNDLE=<not set>
              SSL_CERT_FILE=<not set>
                  USER_PATH=/software/python/conda3/bin:/software/java/java11/bin:/sched/sge/sge-2
                            011-11j/bin/linux-x64:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbi
                            n:/opt/cycle/jetpack/bin:/opt/mssql-tools18/bin:/shared/home/ipushel/.
                            local/bin:/shared/home/ipushel/bin:/bin:/usr/bin:/sbin:/usr/sbin:/usr/
                            local/bin:/usr/local/sbin
 
       active environment : base
      active env location : /shared/home/ipushel/.cache/R/basilisk/1.10.2/0
              shell level : 1
         user config file : /shared/home/ipushel/.condarc
   populated config files :
            conda version : 4.12.0
      conda-build version : not installed
           python version : 3.8.13.final.0
         virtual packages : __linux=3.10.0=0
                            __glibc=2.35=0
                            __unix=0=0
                            __archspec=1=x86_64
         base environment : /shared/home/ipushel/.cache/R/basilisk/1.10.2/0  (writable)
        conda av data dir : /shared/home/ipushel/.cache/R/basilisk/1.10.2/0/etc/conda
    conda av metadata url : None
             channel URLs : https://conda.anaconda.org/conda-forge/linux-64
                            https://conda.anaconda.org/conda-forge/noarch
                            https://repo.anaconda.com/pkgs/main/linux-64
                            https://repo.anaconda.com/pkgs/main/noarch
                            https://repo.anaconda.com/pkgs/r/linux-64
                            https://repo.anaconda.com/pkgs/r/noarch
            package cache : /shared/home/ipushel/.cache/R/basilisk/1.10.2/0/pkgs
                            /shared/home/ipushel/.conda/pkgs
         envs directories : /shared/home/ipushel/.cache/R/basilisk/1.10.2/0/envs
                            /shared/home/ipushel/.conda/envs
                 platform : linux-64
               user-agent : conda/4.12.0 requests/2.27.1 CPython/3.8.13 Linux/3.10.0-1160.83.1.el7.x86_64 ubuntu/22.04.2 glibc/2.35
                  UID:GID : 3095:10000
               netrc file : None
             offline mode : False

  An unexpected error has occurred. Conda has prepared the above report.

  Upload successful.
  Error: Error creating conda environment '/shared/home/ipushel/.cache/R/basilisk/1.10.2/zellkonverter/1.8.0/zellkonverterAnnDataEnv-0.8.0' [exit code 1]
  Execution halted

Work dir:
  /mnt/scratch/work/41/2383ce85763b40edbaf4b010bee2bb

 Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

-- Check '.nextflow.log' file for details

[jashapiro]

I think it would be helpful if irina could send us her /shared/home/ipushel/.condarc file. I have a sense that may be where the issue lies. Looking briefly at the channel urls, I don't see one for bioconda, so my guess is that is what is missing. Not sure why basilisk doesn't handle that internally as I would expect it to, but as I said, this is a guess.

[jashapiro]

While Irina was able to run at least one sample successfully after setting up fresh, I do have a potential solution in AlexsLemonade/scpcaTools#202