Spades container issue

[jodyphelan]

When running mmadeploy I am getting an issue on the spades assembly of SRR25448586.

From the job log it has an issue getting the version of spades:

[shovill] Using trimmomatic - /path/to/mmadeployment/conda/344922d9ef4bb4235935defef70a887e_/bin/trimmomatic | 0.41
[shovill] Using velvetg - /path/to/mmadeployment/conda/344922d9ef4bb4235935defef70a887e_/bin/velvetg | Version 1.2.10
[shovill] Using velveth - /path/to/mmadeployment/conda/344922d9ef4bb4235935defef70a887e_/bin/velveth | Version 1.2.10
[shovill] Can't parse spades version from: Traceback (most recent call last):

When I try to run spades from within the container I see that spades doesn't run with this issue:

Traceback (most recent call last):
  File "/path/to/mmadeployment/conda/344922d9ef4bb4235935defef70a887e_/bin/spades.py", line 26, in <module>
    import support
  File "/path/to/mmadeployment/conda/344922d9ef4bb4235935defef70a887e_/share/spades/spades_pipeline/support.py", line 23, in <module>
    from distutils.version import LooseVersion
ModuleNotFoundError: No module named 'distutils'

This is because distutils has been removed from python since v3.12 but the spades recipe on bioconda doesn't set any upper limit on the python version (only >=3.8). This could be fixed by either pinning a specific version of python (>=3.8,<=3.12) or finding another way to install distutils

[KasperThystrup]

Damn. Does the conda-versions rule provide the spades version (a tsv file) in the deploy folder?

In other words which version of spades?

(Alternate route conda activate /path/to/mmadeployment/conda/344922d9ef4bb4235935defef70a887e_ then spades --version )

[KasperThystrup]

I wish to confirm the version, if it's the latest, a third approach is to update the bioconda/meta.yaml dependencies for spades.

[jodyphelan]

It is version 3.15.5

[KasperThystrup]

Yup, Latest should be 4.3

I was trying to avoid versioning the environments, to ensure that latest pkg versions can be installed, but it seems Micromamba silently installs the wrong versions without letting us know.