utils

Utility shell scripts used for Bioconductor maintenance workflows.

Most scripts assume a local Bioconductor working tree rooted at ~/bioc and SSH access to:

• git.bioconductor.org
• github.com:Bioconductor/*

Repository contents

Environment setup

• setBIOC.sh
  Exports shared variables used by other scripts (BIOC, BBS_HOME, PYTHONPATH, GIST_FOLDER).

Package scanning and migration helpers

• find_keywords.sh
  Scans source files for legacy BiocInstaller/biocLite keywords.
• find_list_packages.sh [software|data-experiment|workflows]
  Builds package lists (saved in the gist folder) based on keyword matches.
• find_valid.sh [packages] [search|line|package]
  Inspects commit history for valid/biocVersion updates in selected packages.
• replace_biocLite.sh
  Rewrites legacy BiocInstaller/biocLite usage to BiocManager calls in the current package directory.
• replace_alt_keywords.sh
  Rewrites alternate legacy helpers (for example biocinstallRepos, biocValid, biocVersion) to BiocManager equivalents.
• fix_repos.sh <pkg_type> <replace|reset|diff|push|status> [packages] [commit_message]
  Runs bulk actions across package repositories (replace, reset, inspect, commit/push, status).

Repository cloning helpers

• clone_git.sh <package>
  Clones a Bioconductor package from GitHub and adds the Bioconductor git remote as upstream.
• clone_repos.sh <branch>
  Uses the Bioconductor manifest to clone/pull many package repositories for a branch.
• clone_check.sh <package>
  Clones one package from git.bioconductor.org and runs keyword scanning.

Review, testing, and release utilities

• biocreview.sh <package_dir>
  Runs package build/check/BiocCheck using local aliases from ~/.bash_aliases.
• testplatforms.sh [r-version]
  Builds and checks BiocManager against one or more local R builds (defaults: 4-4, 4-5, devel).
• TestBiocManager.sh
  Builds/checks BiocManager across local old/release/devel R setups.
• anvil_test_all.sh
  Builds/checks AnVIL packages (AnVILBase, AnVIL, AnVILGCP, AnVILAz) using a local R install.
• version_bump.sh
  Increments the patch component in DESCRIPTION (Version: line), commits the change.
• tag_release.sh
  Example commands for manual git tag creation/push.
• dock.sh <release|tag>
  Starts a Bioconductor Docker image with host library mounts.

Basic usage

Run scripts from your Bioconductor working directory context:

bash ./utils/find_list_packages.sh software
bash ./utils/fix_repos.sh software replace
bash ./utils/testplatforms.sh 4-5

Some scripts source ./utils/setBIOC.sh, so they expect to run from a directory where utils/ is a direct child (commonly ~/bioc).