[OlgaPushkarev]

Summary

Removes the remaining lab-, cluster- and study-specific content so the public-content guard (CI) passes. main has failed this check since the 29 September commit: the workflow scans the whole tree, and 129 hits were left in 15 files.

First of three stacked PRs (please merge in order):

1. Remove remaining lab- and study-specific content #18 (this PR): lab-content cleanup.
2. Format all Python files with ruff (format-only) #19: ruff format of all Python files (format-only).
3. Support non-perturbed scRNA-seq and mouse data #20: support for non-perturbed scRNA-seq and mouse data.

Changes

• Annotation runners (C_Annotation/*/run_*.sh):
  • Use PIPELINE_ROOT for SCRIPT_DIR. This also fixes paths into an AGeneTic/ folder that doesn't exist in the repo, so these runners did not work from a fresh clone.
  • Activate conda with conda shell.bash hook instead of a personal install.
  • Use <partition>, and quoted /path/to/... placeholders for result directories.
• run_add_umap.sh:
  • PIPELINE_ROOT-relative SCRIPT_DIR.
  • The log directory is configurable (ADD_UMAP_LOG_DIR, default ./add_umap_logs) and is passed explicitly when the script resubmits itself.
  • <partition> / <your_email> placeholders.
  • Sizing notes no longer name datasets; instructions added for the manual sbatch path.
• gpe_export.py: reads the GeneProgramExplorer location from a GPE_DIR environment variable, with a clear error when it is missing.
• Wording: generic text in two test usage blocks, search_nature.py, a --cell_type help example, and two comments/messages that named specific datasets.
• CHANGELOG entry.

Testing

• python3 tools/check_no_lab_specific_content.py (full tree, as in CI): no hits.
• All tracked .sh files pass bash -n, and every script path they reference exists. All tracked .py files compile.
• The two HTML no-perturb test files pass (8/8).
• gpe_export raises the intended error when GPE_DIR is wrong.

The annotation runners and gpe_export.py pointed to a collaborator's personal folders, so local copies that relied on those paths need PIPELINE_ROOT / GPE_DIR set.

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