Mc pipeline/sync brca exchange pipeline #1593
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…rade to python 3.13, but there's no support yet for pysam
Changed base image from python:3.9-buster to python:3.12-bookworm to complete the Python 3.12 migration for the pipeline environment. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
- Updated Dockerfile: removed deprecated python-lzo and redundant python3/pip packages, updated netcat to netcat-openbsd, upgraded pip to 24.3.1 for Python 3.12 - Enhanced generate_release.py: added git fetch and fallback logic to properly checkout any named branch from GitHub, including remote branches 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
- Updated Dockerfile grep patterns to use "^numpy" and "^cython" to match only lines starting with package names, avoiding inline comments - Updated numpy version to >=1.24.3,<2.0 appropriate for Python 3.12 - Removed inline comment from numpy requirement that was causing grep to match comment syntax This fixes the build error: "Invalid requirement: '#': Expected package name at the start of dependency specifier" 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
- Updated hypothesis from 5.6.0 to >=6.98.0 - Updated pytest from 5.4.1 to >=8.0.0 (matches requirements.txt) - Updated pytest-cov from 2.8.1 to >=4.1.0 (matches requirements.txt) - Updated coverage from 5.0.4 to >=7.4.0 - Removed duplicate mock package (already in requirements.txt) This fixes the dependency conflict error: "Cannot install pytest==5.4.1 and pytest>=8.0.0" 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
- Changed /opt/brca-exchange to /opt/brca-exchange-kb in multiple locations - Updated mount check and working directory paths 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
If the SSH connection to the pipeline machine fails, the Makefile will now automatically fall back to downloading LOVD data from the backup URL at brcaexchange.org. This improves reliability when the primary access method is unavailable. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
The template was trying to use brca_2024 as a variable instead of a string literal, causing UTA_PG_PW to be empty. This resulted in a malformed docker command when starting the UTA container. Now properly sets the PostgreSQL password environment variable in KEY=VALUE format. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
Changed 'lauch_seqrepo.sh' to 'launch_seqrepo.sh' to match the actual filename in utilities/ directory. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
- Updated six from 1.14.0 to >=1.16.0 for better Python 3.12 compatibility - Added explicit installation of six before numpy/cython in Dockerfile - Ensures six.moves is available when pandas and other packages need it Fixes: ModuleNotFoundError: No module named 'six.moves' 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
- Update yoyo-migrations from 7.0.1 to >=9.0.0 (removes iniherit dependency) - Remove iniherit==0.3.9 (incompatible with Python 3.12 SafeConfigParser) - Update biocommons.seqrepo from 0.6.6 to >=0.6.9 (fixes timestamp deprecation) Fixes AttributeError: module 'configparser' has no attribute 'SafeConfigParser' 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
- Update coloredlogs from ==14.0 to >=15.0 - Required by biocommons.seqrepo>=0.6.9 which depends on coloredlogs~=15.0 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
- Update tqdm from ==4.43.0 to >=4.66 - Required by biocommons.seqrepo>=0.6.9 which depends on tqdm~=4.66 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
- Update humanfriendly from ==8.0 to >=9.1 - Required by coloredlogs>=15.0 which depends on humanfriendly>=9.1 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
- Update UTA version from 20210129b to 20241220 - Update UTA password variable to uta_password - Update UTA volume to uta_vol - Remove deprecated VICTOR_IMAGE configuration sections These updates align the pipeline with the latest versions of UTA and remove unused configuration for improved maintainability. 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude Sonnet 4.5 <[email protected]>
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