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deTELpy setup notes

Environment created for upstream deTELpy before PIRATE work.

Sources checked

  • Upstream repo: https://git.mpi-cbg.de/tothpetroczylab/detelpy
  • PyPI package: deTELpy 0.1.13
  • README notes: Python 3.9-3.11 supported; Python 3.12 not supported; Mono required for eTEL Thermo RAW handling; FragPipe/MSFragger/Philosopher/IonQuant required for rTEL, but upstream says rTEL/FragPipe is Linux-only and not macOS-supported.

Local environment

  • Repo: /Users/gini/.openclaw/workspace/ms-proteomics/detelpy
  • Venv: /Users/gini/.openclaw/workspace/ms-proteomics/detelpy/.venv
  • System deps installed with Homebrew: mono, openjdk@17
  • Runtime env vars used:
    • PATH="/opt/homebrew/opt/openjdk@17/bin:$PATH"
    • JAVA_HOME="/opt/homebrew/opt/openjdk@17/libexec/openjdk.jdk/Contents/Home"
    • MONO_GAC_PREFIX="/opt/homebrew"

Dependency fix needed

deTELpy depends on spectrum_utils[iplot]==0.3.5, which allowed pyteomics==5.0. On Python 3.9 that fails at import time (TypeError from PEP604 union syntax). Fixed locally by pinning:

python -m pip install 'pyteomics<5'

Installed version: pyteomics 4.7.5.

Verification commands run

python -m pytest deTEL/tests/test_run_deTEL.py -q

Result: 10 passed.

CLI smoke test commands using bundled upstream test resources:

python -m deTEL eTEL -f deTEL/tests/resources/s228c_orf_cds.fasta -psm deTEL/tests/resources/psm.tsv -s deTEL/tests/resources/results_ionquant2 -o setup_test/etel_output -p PXD018591 -tol 0.005
python -m deTEL mTEL -f deTEL/tests/resources/results_ionquant2 -r deTEL/tests/resources/tRNA_count/yeast_tRNA_count.csv -o setup_test/mtel_output -s 250 -p 100 -c 4.2e-17 -t 10 -b 100 -nb -1 -a n
python -m deTEL rTEL --generate-config --config_dir setup_test/rtel_config

Outputs written under setup_test/.