souporcell.py can't find tensorflow

[jrkirk61]

I tried pulling the singularity image of this on a Linux-based (Rocky Linux 8.5) computer cluster. I got a couple of warnings but wasn't sure if they were normal.

$ singularity pull --arch amd64 library://wheaton5/souporcell/souporcell:release
INFO:    Downloading library image
2.1GiB / 2.1GiB [=====================================================================================] 100 % 36.2 MiB/s 0s
WARNING: integrity: signature not found for object group 1
WARNING: Skipping container verification

I then tried testing some of the executables and a few worked just fine, but this one did not:

$ singularity exec souporcell_release.sif souporcell.py -h
Traceback (most recent call last):
  File "/opt/souporcell/souporcell.py", line 5, in <module>
    import tensorflow as tf
ModuleNotFoundError: No module named 'tensorflow'

Can you let me know what could be going on here?

[wheaton5]

Souporcell.py is the deprecated legacy clustering which has been replaced by a version written in rust. Everything flows from souporcell_python.py so it will run everything else.

[wheaton5]

Those warnings are normal

[cjfields]

@wheaton5 I'm assuming you mean souporcell_pipeline.py instead of souporcell_python.py? The former is in the container, the latter is not:

$ singularity exec /home/groups/hpcbio/singularity/souporcell_release_2.5.sif souporcell_pipeline.py -h
usage: souporcell_pipeline.py [-h] -i BAM -b BARCODES -f FASTA -t THREADS -o
                              OUT_DIR -k CLUSTERS [-p PLOIDY]
                              [--min_alt MIN_ALT] [--min_ref MIN_REF]
                              [--max_loci MAX_LOCI] [--restarts RESTARTS]
                              [--common_variants COMMON_VARIANTS]
                              [--known_genotypes KNOWN_GENOTYPES]
                              [--known_genotypes_sample_names KNOWN_GENOTYPES_SAMPLE_NAMES [KNOWN_GENOTYPES_SAMPLE_NAMES ...]]
                              [--skip_remap SKIP_REMAP] [--no_umi NO_UMI]
                              [--umi_tag UMI_TAG] [--cell_tag CELL_TAG]
                              [--ignore IGNORE] [--aligner ALIGNER]...

$ singularity exec /home/groups/hpcbio/singularity/souporcell_release_2.5.sif souporcell_python.py -h
FATAL:   "souporcell_python.py": executable file not found in $PATH

[wheaton5]

Yes, my bad. This is all in the docs tho.

[jrkirk61]

Thanks!