Issue: Consistent error with installation (singularity)

[lkearney001]

When building a Docker image the following error occurs. Please assist if possible.

-- lawrence

podman build -t aertslab/scenicplus:latest . -f scenicplus/Dockerfile

Preparing metadata (pyproject.toml): started
Preparing metadata (pyproject.toml): finished with status 'error'
error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully.
│ exit code: 1
╰─> [4 lines of output]
Requirement already satisfied: numpy>=1.17 in /tmp/pip-build-env-mw6zttkb/overlay/lib/python3.8/site-packages (1.24.2)
error in MACS2 setup command: 'install_requires' must be a string or list of strings containing valid project/version requirement specifiers; Expected end or semicolon (after name and no valid version specifier)
numpy>=>=1.17
^
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.
Error: error building at STEP "RUN pip install --no-cache-dir --upgrade pip wheel && pip install --no-cache-dir numpy==1.22 && pip install --no-cache-dir MACS2 && pip install --no-cache-dir scipy==1.8.0 && pip install --no-cache-dir Cython && pip install --no-cache-dir fitsne && pip install --no-cache-dir papermill && pip install --no-cache-dir igv_jupyterlab && pip install --no-cache-dir bs4 && pip install --no-cache-dir lxml && pip install --no-cache-dir tspex && pip install --no-cache-dir plotly && pip install --no-cache-dir kaleido && pip install --no-cache-dir pyvis && pip install velocyto && pip install --no-cache-dir pygam && pip install --no-cache-dir fa2 && pip install --no-cache-dir scanpy==1.8.2 && pip install --no-cache-dir -r /tmp/requirements.txt": error while running runtime: exit status 1

[lkearney001]

Still hoping I can get some help with this one, really need to deploy this as a singularity container.

-- lawrence

[SeppeDeWinter]

Hi @lkearney001

Your issue sounds similar to this one: #101

The solution I gave there might be able to help you.

Best,

Seppe

[lkearney001]

Seppe,
Yes, it does sound similar, I did see it, but how is can it be applied to the singularity container build issue when the install set is referenced in the docker repo (aertslab/scenicplus:latest)?

-- lawrence

[pajucon]

Remove the original pip install MACS line from the dockerfile.
Substitute with a pip install from the local corrected MACS directory (reference the pip local installs lower in the dockerfile).

[hangarbait]

... ty vry much. I'll test and advise of the result.

-- lawrence