common_paths.yml.sample

# common_paths.yml — machine-local mapping of citation prefixes to filesystem
# paths and (optionally) GitHub repo metadata for permalink rendering.
#
# Copy to `common_paths.yml` (gitignored) and adjust paths to your machine.
#
# In note bodies, write corpus citations inside inline code as:
#
#   `$NAME/relative/path/to/file.ext`
#   `$NAME/relative/path/to/file.ext:545`
#   `$NAME/relative/path/to/file.ext:545-560`
#
# Per-entry fields:
#   path         — absolute filesystem path on this machine. ~ expands to $HOME.
#   repo         — optional. "<owner>/<repo>" on github.com. When set, the
#                  Astro renderer rewrites citations into clickable permalinks.
#   ref          — optional, requires repo. branch / tag / commit SHA used to
#                  build the permalink. Default: "main". Pin to a SHA for
#                  stable links; pin to a branch for fresh-but-rotting links.
#   path_prefix  — optional, requires repo. Prepended to the relative path
#                  when constructing the GitHub URL. Use when the local
#                  checkout is a subset / transformed view of the upstream
#                  repo (the cited file's *local* path differs from its path
#                  in the repo).
#
# Naming convention: uppercase letters, digits, underscores. The leading `$`
# in citations is the marker; the rest is matched against the keys below
# case-insensitively.

iwc:
  path: ~/projects/repositories/iwc
  repo: galaxyproject/iwc
  ref: main

# $IWC_FORMAT2 and $IWC_SKELETONS resolve automatically to
# <foundry-checkout>/workflow-fixtures/{iwc-format2,iwc-skeletons} — built in
# to scripts/lib/common-paths.ts, no user config needed. Override here if
# you keep the corpus elsewhere.

galaxy:
  path: ~/projects/repositories/galaxy
  repo: galaxyproject/galaxy
  ref: dev

# Temporary source for Galaxy prompt work before the upstream branch merges.
galaxy_dannon:
  path: ~/projects/repositories/dannon-galaxy
  repo: dannon/galaxy
  ref: 69d0c697b495b7f16b1475c00c8bfbd7b9bfa85e

tools_iuc:
  path: ~/projects/repositories/tools-iuc
  repo: galaxyproject/tools-iuc
  ref: main

planemo:
  path: ~/projects/repositories/planemo
  repo: galaxyproject/planemo
  ref: master

gxformat2:
  path: ~/projects/repositories/gxformat2
  repo: galaxyproject/gxformat2
  ref: main

galaxy_tool_util_ts:
  path: ~/projects/repositories/galaxy-tool-util-ts
  repo: jmchilton/galaxy-tool-util-ts
  ref: main