Add protein_compare to folding_prod container (conda-predict env)

[wilke]

Summary

The App-PredictStructure.pl service script calls python -m protein_compare characterize in run_report() to generate structure characterization reports (HTML + JSON). However, protein_compare is not installed in the folding_prod.sif container's conda-predict environment, so report generation silently fails.

Current state

• protein_compare lives in a separate standalone container (protein-compare.sif), built from protein_structure_analysis/container/protein-compare.def
• The CWL workflows use protein-compare.sif as a separate step — this works
• The Perl service script assumes protein_compare is available in the same Python environment as predict-structure — this does not work

Proposed fix

Install protein_compare into the existing conda-predict environment as a container build concern (not a Python dependency of predict-structure). This keeps the packages conceptually separate while making them co-available at runtime.

In the container def layer (reqts-predict-structure.def or equivalent):

conda activate /opt/conda-predict
pip install --no-cache-dir \
    "protein_compare @ git+https://github.com/BV-BRC/protein_structure_analysis.git"

Version compatibility (verified)

Shared dependencies — no conflicts:

Package	conda-predict	protein_compare requires
biopython	1.87	>=1.81
numpy	2.4.4	>=1.24
pandas	3.0.2	>=2.0
click	8.3.1	>=8.1

New packages needed: scipy, matplotlib, seaborn, tmtools, joblib

Also needed

• System packages for DSSP and matplotlib rendering: dssp, libgl1, libglib2.0-0, libfontconfig1
• CCD compound data for DSSP: curl -o /var/cache/libcifpp/components.cif https://files.wwpdb.org/pub/pdb/data/monomers/components.cif
• Note: Debian Trixie replaced libgl1-mesa-glx with libgl1

Acceptance criteria

• apptainer exec folding_prod.sif /opt/conda-predict/bin/python -m protein_compare --help succeeds
• App-PredictStructure.pl report generation produces HTML and JSON output
• No version conflicts with existing predict-structure dependencies