galaxy/.gitignore

.hg*

# Downloaded and locally built eggs
eggs
scripts/scramble/build
scripts/scramble/lib
scripts/scramble/archives

# Python virtualenv
.venv*/

# Python build artifacts
build
dist
*.egg-info/
.eggs

# Generated static content
lib/galaxy/web/framework/static/maps
lib/galaxy/web/framework/static/scripts
lib/galaxy/web/framework/static/style
lib/galaxy/web/framework/meta.json

# Misc. data, config, cache files
/database/

# Python bytecode
*.pyc

# Galaxy runtime files
*.lock
*.log
*.pid

# Celery state files
celerybeat-schedule
celery-beat-schedule
celerybeat-schedule.db

# Tool Shed runtime files
tool_shed_webapp.lock
tool_shed_webapp.log
tool_shed_webapp.pid
hgweb.config*
lib/tool_shed/scripts/bootstrap_tool_shed/user_info.xml

# Reports runtime files
reports_webapp.lock
reports_webapp.log
reports_webapp.pid

# Jupyter runtime files
.ipynb_checkpoints

# Config files
universe_wsgi.ini
reports_wsgi.ini
reports.ini
tool_shed_wsgi.ini
datatypes_conf.xml
tool_conf.xml
external_service_types_conf.xml
migrated_tools_conf.xml
shed_tool_conf.xml
tool_data_table_conf.xml
tool_sheds_conf.xml
integrated_tool_panel.xml
openid_conf.xml
shed_tool_data_table_conf.xml
job_conf.xml
data_manager_conf.xml
shed_data_manager_conf.xml
object_store_conf.xml
job_metrics_conf.xml
workflow_schedulers_conf.xml
client_build_hash.txt
config/*
config/plugins/interactive_environments/**/*.ini
config/plugins/**/.cache
config/plugins/**/.parcel-cache
config/plugins/visualizations
!config/plugins
static/welcome.html.*
static/welcome.html
lib/galaxy_test/selenium/jupyter/galaxy_selenium_context.yml

# Tool data
tool-data/annotation_profiler_options.xml
tool-data/annotation_profiler_valid_builds.txt
tool-data/gatk_annotations.txt
tool-data/gd.restriction_enzymes.txt
tool-data/gd.species.txt
tool-data/shared/igv/igv_build_sites.txt
tool-data/shared/rviewer/rviewer_build_sites.txt
tool-data/shared/ncbi/builds.txt
tool-data/shared/ucsc/builds.txt
tool-data/shared/ucsc/manual_builds.txt
tool-data/shared/ensembl/builds.txt
tool-data/shared/ucsc/publicbuilds.txt
tool-data/shared/ucsc/ucsc_build_sites.txt
tool-data/*.loc
tool-data/genome/*
tool-data/*.sample
tool-data/testtoolshed.g2.bx.psu.edu/
tool-data/toolshed.g2.bx.psu.edu/
tool-data/**/*.fa

# Test output
.pytest_cache/
assets/
test-data-cache
run_api_tests.html
run_cwl_tests.html
run_framework_tests.html
run_framework_workflows_tests.html
run_functional_tests.html
run_integration_tests.html
run_playwright_tests.html
run_selenium_tests.html
run_toolshed_tests.html
test/tool_shed/tmp/*
.coverage
htmlcov
run_unit_tests.html
test/unit/**.log
.tox
tool_test_output.html
tool_test_output.json

# Project files
*.kpf
.idea
.vscode
client/**/jsconfig.json
vetur.config.js
.pre-commit-config.yaml
galaxy.code-workspace

# Chrom len files
*.len

# JARs
tool-data/shared/jars/

# JS, Local node_modules, and bower_components directories
static/maps
static/plugins
static/scripts
node_modules
bower_components
client/src/libs/*

# Old galaxy client location
client/galaxy

# Documentation build files
doc/build
doc/schema.md
doc/source/admin/config_logging_default_yaml.rst
doc/source/dev/schema.md
doc/source/dev/plantuml.jar
client/docs/dist

# Webpack stats
client/webpack-stats.json

# Packages
packages/*/build
packages/*/dist
packages/meta/requirements.txt

# Standalone script + main, or build into dist
config/plugins/**/static/dist
config/plugins/**/static/script.js
config/plugins/**/static/main.css
config/plugins/**/static/script.css
config/plugins/**/static/plugin_build_hash.txt
config/plugins/**/static/*.map

# Viz-specific build artifacts to ignore (until these are removed from codebase)
config/plugins/visualizations/annotate_image/static/jquery.contextMenu.css
config/plugins/visualizations/nvd3/nvd3_bar/static/nvd3.js
config/plugins/visualizations/scatterplot/static/scatterplot.js
config/plugins/visualizations/tiffviewer/static/

# CWL conformance tests
lib/galaxy_test/api/cwl/test_cwl_conformance_v1_?.py
test/functional/tools/cwl_tools/v1.?/

# Involucro tool
involucro

# Claude Code local settings
.claude/settings.local.json

# GTN search database (downloaded on first use)
lib/galaxy/agents/gtn/data/gtn_search.db

# Misc
*.orig
.DS_Store
*.rej
*~

# Agent eval runner: per-user model config (real keys live in env, but be safe)
test/evals/models.yaml
# Eval result artifacts -- keep baselines you care about somewhere outside
# the repo. Filenames encode the repo SHA they were generated from, so any
# baseline file pairs back to the exact commit it came from.
test/evals/results/*
!test/evals/results/.gitkeep