Build error with `--build-template conda/micromamba:v2` for singularity

[mashehu]

When trying

wave --conda-file ~/drugresponseeval/modules/local/evaluate_find_max/environment.yml 
		--freeze
        --platform linux/arm64 
		-o yaml 
		--build-template conda/micromamba:v2 
		--log-level DEBUG 
		--singularity
        --await

I get the following build error (see build page https://wave.seqera.io/view/builds/bd-4ad8f1096976ef9c_6):

INFO:    Extracting OCI image...
INFO:    Inserting Singularity configuration...
INFO:    Copying /opt/conda.tar.gz to /opt/conda.tar.gz
INFO:    Running post scriptlet
+ cd /opt
+ tar xzf conda.tar.gz
tar: conda/conda-meta: Cannot change mode to rwxrwxrwx: No such file or directory
tar: conda/pkgs/cache: Cannot change mode to rwxrwsr-x: No such file or directory
tar: conda/pkgs/_openmp_mutex-4.5-2_gnu/info/recipe/parent/tests/fortomp: Cannot change mode to rwxrwxr-x: No such file or directory
...

It builds fine with the default template, but I want the pip dependencies from my environment.yml in the lock file.

I am aware of the limitation related to tar and singularity mentioned in the docs, but the default base images comes with tar so should be fine:

docker run mambaorg/micromamba:1.5.10-noble  tar --version
tar (GNU tar) 1.35
Copyright (C) 2023 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.

[munishchouhan]

@mashehu thanks for reporting the error, we will look into it and get back to you

[munishchouhan]

@mashehu I have created a fix for this #972
Can you please try this image oras://docker.io/hrma017/python_pip_drevalpy:bwa_salmon--9ec0f9cfe319ff4c?
https://wave.dev-seqera.io/view/builds/bd-9ec0f9cfe319ff4c_1

Please let me know, if it works or not?

[mashehu]

The environment file on the linked build page shows different dependencies. I especially want to test environment files with pip dependencies, which don't show up in the conda lock file when using the default template.

[munishchouhan]

The environment file on the linked build page shows different dependencies. I especially want to test environment files with pip dependencies, which don't show up in the conda lock file when using the default template.

is it possible to share the reproducer?

[mashehu]

I want to build the conda lock files for the following module https://github.com/mashehu/drugresponseeval/blob/update-containers/modules/local/collect_results/environment.yml

[munishchouhan]

@mashehu please try this oras://docker​.io/hrma017/build:python-3​.13_pip-25​.3_drevalpy-1​.4​.1--30d808349ca2f2ca
https://wave.dev-seqera.io/view/builds/bd-30d808349ca2f2ca_1

[mashehu]

Can't to seem to access the conda lock file via https://wave.seqera.io/v1alpha1/builds/bd-30d808349ca2f2ca_1/condalock . Was that not generated somehow?

[munishchouhan]

Weird Condalock was parsed in for the same build in previous iteration, but not in this one. Image name is not very good, i forgot to chnage it but deps are correct
https://wave.dev-seqera.io/view/builds/bd-4109fc03464e9c7e_1
You can get the condalock file from here
https://wave.dev-seqera.io/v1alpha1/builds/bd-4109fc03464e9c7e_1/condalock

[mashehu]

Thanks, this worked now!
Unfortunately this template also doesn't include pip dependencies in the conda lock file.
The pixi one does, but I ran into another bug there I think, time for another issue 😬