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koopa 0.5.6 (2019-09-18)

New scripts

  • gencode-fasta and gencode-gtf Python scripts for downloaded GENCODE genome annotations. Currently supports Homo sapiens and Mus musculus.
  • (Azure) link-msigdb: Shared MSigDB file annotation utility.

Minor changes

  • Improved global activation of general exports, including EDITOR, which defines the default text editor. "vim" is recommended by default but "emacs" is also a good choice.

koopa 0.5.5 (2019-09-09)

Major changes

  • Updater now checks for: oh-my-zsh, spacemacs symlinks in config directory.

Minor changes

  • Added install support for ChromHMM.
  • Bug fix for directory creation in Python cellar script.
  • ZSH configuration improvements.

koopa 0.5.4 (2019-09-05)

Minor changes

  • Improved alias handling for zsh configuration.
  • Added additional useful aliases and functions from Stephen Turner's oneliners guide for bioinformatics.
  • Initial configuration support for autojump, currently limited to zsh. Will test and add bash support in a future update.

koopa 0.5.3 (2019-08-28)

Minor changes

  • Improved zsh activation and oh-my-zsh configuration handling when koopa is active inside /etc/profile.d/ on Linux (i.e. RHEL 7).

koopa 0.5.2 (2019-08-18)

This release improves prompt consistency between zsh and bash.

Minor changes

  • Reworked prompt string configuration. Now automatically updates correctly when either a conda environment or Python virtual environment are loaded. Removed shell version and disk usage from the prompt.
  • Updated zsh shell configuration to use our custom, more minimal koopa prompt instead of Pure prompt. This prompt is visually identical to our bash PS1.
  • Reduced the number of available string returns from main koopa function. Instead, these are now called more consistently using internal prefixes. (e.g. _koopa_cellar_prefix instead of koopa cellar-prefix).

koopa 0.5.1 (2019-08-15)

Minor changes

  • Bug fixes for koopa activation inside a subshell (e.g. tmux or slurm queue).

koopa 0.5.0 (2019-08-14)

Major changes

  • Koopa now attempts to source user configuration files prior to activation. This enables better passthrough of user-defined configuration variables.
  • Simplified dotfiles configuration handling. Now need to install manually using --dotfiles flag or can use install-dotfiles script after installation.
  • Fixed shell configuration when EDITOR="emacs".

koopa 0.4.6 (2019-08-01)

New scripts

  • ftp-mirror: Script that helps quickly mirror an FTP directory using wget.
  • install-rcheck: Utility for quickly checking R packages.

Minor changes

  • Reworked the file paths of some dot files related to vim and zsh config.
  • Improved docker-run-image workdir configuration.
  • Improved shell checks, following shellcheck 0.7 release updates.
  • Relaxed checks in Debian and Fedora headers when running as sudo user.

koopa 0.4.5 (2019-07-29)

Minor changes

  • Improved detection and handling of unbound variables during installation and activation of koopa.

koopa 0.4.4 (2019-07-28)

New scripts

  • ffmepeg-alac-to-flac, ffmepeg-flac-to-alac: Lossless audio conversion.
  • move-into-dated-dirs-by-filename: Automatically move files containing a date (e.g. 2019-07-28-12-01-59.txt) into dated subdirectories (e.g. 2019/07/28/).
  • move-into-dated-dirs-by-timestamp: Automatically move files into a dated subdirectory according to its timestamp.
  • sox-downsample: Utilty script for easily downsampling high resolution audio.

Darwin (macOS)-specific

  • delete-adobe-bridge-cache: Delete Adobe Bridge cache files.
  • dotfile-icloud: Dot file utility for linking from iCloud, instead of our dotfiles git repo.
  • update-defaults: Utility for setting recommended defaults. Modifies some finder settings, screen shots path, etc.


  • install-git-lfs: Utility script for installing Git LFS.


  • Added additional packages to install via yum by default.
  • install-cellar-gdal: New recipe required to install rgdal R package.
  • install-cellar-proj: New recipe required to install rgdal R package.

Major changes

  • Installation will now clone private scripts and docker recipes. The activation script now knows to look for these and will add bin/ directories to PATH.

Minor changes

  • Reworked linter engine to check for maximum of 80 characters per line.
  • Improved internal update timestamp consistency across files.
  • Improved shared Renviron and Rprofile site configuration files.

koopa 0.4.3 (2019-07-25)

New scripts

  • docker-run-image: Useful utility script for booting a Docker image.
  • patch-bcbio: Utility for patching bcbio development installation from GitHub codebase.
  • upgrade-bcbio: Utilty for upgrading bcbio on a virtual machine.

koopa 0.4.2 (2019-07-12)

Minor changes

  • Improved automatic XDG configuration in ~/.config/koopa. Needed to update configuration of R symlink.

koopa 0.4.1 (2019-07-11)

Major changes

  • Removed support for ksh. This shell does not support usage of local variables inside of functions, which are tremendously useful, and prevent accidental variable overwrites. Therefore, we're restricting support for bash and zsh at the moment.
  • Improved Fedora install scripts to support RHEL 8. Also updated Docker install script to support RHEL 8.

Minor changes

  • Harden scripts to pass shellcheck.
  • Switch back to using -n instead of ! -z consistently for POSIX code. Double checking, this works correctly with latest version of ZSH.
  • Sort arrays using mapfile, which is recommended by shellcheck.
  • Improve shebang detection inside recursive shellcheck script.
  • Added fixme/todo comments detection in linter script.
  • Updated recommended program versions.
  • Improved version checks inside check.R script.

New programs

  • Added copy-bam-files utility, which makes it easier to quickly set up an IGV session, which requires both *.bam and *.bam.bai files. Previously, this was named cp-bam-files.

koopa 0.4.0 (2019-06-13)

This is the first release supported to work when installed at /usr/local. This enables shared shell configuratino of all users, via configuration in /etc/profile (or /etc/profile.d/) instead of relying on .bash_profile.

Major changes

  • koopa now checks for root and doesn't attempt to activate.
  • Improved dotfile initialization, and no files are overwritten by default.
  • Reworked install script, and added usage accessible via --help.
  • Added uninstall utility script.
  • Reworked activation scripts to support multi-user config.
  • Reworked shared script header approach.
  • Improved automatic /etc/ configuration.

Minor changes

  • KOOPA_HOME path is always expanded, and symlinks are now resolved.
  • Improved Travis CI testing approach.
  • Reorganized workflow scripts.
  • Split out functions into individual scripts.

koopa 0.3.6 (2019-06-05)

Major changes

  • Improved update script.
  • Install koopa using simply install instead of
  • Improved attempt at dotfiles auto-linking during install call.
  • Improved OS-specific PATH exports.
  • Switched to using KOOPA_BUILD_PREFIX and KOOPA_TMP_DIR variables for build scripts.

New programs

  • sudo-install-amzn-base: Recommended initial setup for Amazon Linux 2.
  • sudo-install-debian-base: Recommended initial setup for Debian.
  • sudo-install-fedora-base: Recommended initial setup for Fedora.
  • sudo-update-system scripts for supported operating systems.
  • sudo-install-perl-rename
  • sudo-install-shiny-server

Minor changes

  • Removed attempt at automatic bcbio install detection for Azure. Consider linking current release as recommended in bcbio install instructions.
  • Hardened some additional unbound variables detected in the activation scripts.
  • Reworked bash and zsh activation steps. Namely, removed file.
  • Disabled set +x for some scripts, which was used for testing.
  • Renamed pre-flight check scripts.
  • Hardened zsh setup scripts, using [[ instead of [ consistently.
  • Miscellaneous early return fixes, e.g. for conda and virtualenv detection.
  • Renamed RHEL scripts to use Fedora instead. Improved check support for distros that extend Fedora, such as RHEL 7 and Amazon Linux 2.
  • Simplified shellcheck installation across distros.
  • Improved conda installation messages.

koopa 0.3.5 (2019-06-04)

This version introduces a fair number of changes, in preparation for future v0.4 release series. They should be breaking changes, so we indicated this as a point release instead.

Major changes

  • koopa now clones Mike's dotfiles repo as a submodule, in dotfiles/.
  • Moved install scripts from install/ into nested inside bin/ instead.

Minor changes

  • Reorganized exported scripts in bin/ directory.
  • Improved platform checks and related messages.
  • Moved sudo-* scripts into nested sudo/ directory, to allow conditional access in $PATH export for sudo users only.
  • Improved check-versions script to determine if R is installed. Added additional improvements to the R code for these checks.
  • Azure: rsync-azure-files: Now excluding work/ directories, for bcbio.
  • Initial setup of sudo scripts for RHEL 7.
  • Improved information shown in koopa-info script.

New programs

  • install-doom-emacs: Setup script for doom-emacs.
  • install-genrich: Install Genrich caller for ChIP/ATAC-seq.
  • install-python-virtualenv: Updated to support Python 3.
  • install-rmate: Useful utility for opening remote scripts in VS Code.
  • install-spacemacs: Install script for spacemacs (emacs+vim editor).
  • youtube-mp3, youtube-thumbnail: New youtube-dl-related utility scripts.

Additional files

  • Added support files for fedora ldconfig in etc/ This are particularly useful for configuring programs installed at /usr/local, and for R to correctly pick up library dependencies.

koopa 0.3.4 (2019-05-24)

  • Improved version dependency checks.
  • Added new check-versions program, for additional version checks.
  • Improved build scripts in install/ to use /tmp/ for temp files.
  • New build scripts: bash, coreutils, gnupg, openssl, pass, r, rstudio-server, and zsh.
  • Now using a shared script for simpler build dependency checks.

koopa 0.3.3 (2019-05-08)

  • Renamed all exported scripts to no longer use file extensions. This makes transitioning any bash scripts to python easier, without breaking names.
  • Reworked shellcheck-recursive to check for shell shebang, rather than relying on the file extension.
  • Rewrote download-fasta and download-gtf in Python instead of Bash.

koopa 0.3.2 (2019-04-18)

  • Improved build scripts, and hardened some intended for RedHat Linux.
  • Updated genome build information.
  • Improved bcbio scripts and custom genome builds.
  • New exported scripts:,
  • Added script to build Python from source for RedHat.

koopa 0.3.1 (2019-03-19)

  • Updated to Ensembl release to 95.
  • Updated GENCODE to release human 29 / mouse M20.
  • Updated FlyBase to 2019_01.
  • Added git fetch call.
  • Improved build configuration scripts: emacs, git, gsl, openssl, tmux.
  • Added bcbio system configuration files (bcbio_system.yaml).
  • Improved default run template for bcbio RNA-seq.

koopa 0.3.0 (2019-02-20)

This release overhauls the previous activation method. Refer to the README for details on how to reconfigure your shell profile.

  • Changed activation method to use script at top of repo.
  • Improved support for ksh and zsh shells. Added Travis CI checks.
  • Added native support for zsh pure prompt, including async script. These files are saved in zsh/fpath/.
  • Reorganized bcbio configuration scripts and templates.
  • Completely overhauled system activation method. Additional shell configuration, including prompt string customization is now disabled by default. Refer to the installation instructions for details on how to enable this new optional extra mode.
  • Reorganized installer scripts exported in bin/ including conda scripts,,, etc.

koopa 0.2.8 (2019-02-12)

  • Migrated darwin (macOS)-specific scripts from bash repo to koopa.
  • Migrated Harvard O2 and Harvard Odyssey HPC scripts here from bash repo.
  • Added script for working with Azure Shares (Samba).
  • Added script.
  • Added script.
  • Added script.
  • Reorganized other scripts accessible via bin/.
  • Reorganized activation and system scripts, in preparation for 0.3 release.

koopa 0.2.7 (2019-02-04)

  • Improved shellchecks on workflows.
  • Split out some activation steps into separate scripts.

koopa 0.2.6 (2019-01-23)

  • Added back ".sh" extension for all exported scripts.
  • Updated Travis CI configuration to use shellcheck.
  • Reorganized and improved workflow scripts.

koopa 0.2.5 (2019-01-07)

  • Updated installation instructions to recommend cloning to ~/.koopa.
  • Conda now will only activate when CONDA_DEFAULT_ENV is set in environment. This improves handling in situations for user accounts where we don't want to activate conda in a shared environemnt (e.g. bioinfo account on Azure).

koopa 0.2.4 (2019-01-09)

Major changes

  • Reworked activation script to use POSIX instead of bash conventions. Notably, this involves switching to [ from [[.
  • Early return using return instead of exit when koopa is already active, to prevent accidental lockout on a remote SSH connection.

Minor changes

  • Improved support for ZSH in activation script.
  • Initial commit of NEWS file.
  • Now checking on Travis CI only against master branch.

koopa 0.2.3 (2019-01-01)

Minor changes

  • Improved variable quoting inside bin/ scripts.
  • Reworked activation steps in main script.
  • Deleted reference.txt file in system/.
  • Deleted function scripts inside functions/. Rethinking this approach.

Removed programs

  • Deleted sam_to_bam utility script.

koopa 0.2.2 (2018-12-19)

New programs

  • Added trash utility, which moves files to ~/.Trash, similar to macOS.

Removed programs

  • Removed sudo_install_git and sudo_install_r_cran. Rethinking this approach in a future update.
  • Removed these macOS-specific scripts: brew_cleanup, brew_status, brew_upgrade, install_homebrew, and install_openssl.

New functions

  • Added and utilty functions.

Minor changes

  • Improved error message for unsupported shells in koopa.

koopa 0.2.1 (2018-11-24)

New programs

  • Added git_push_all and git_status_all, corresponding to git_pull_all.

Minor changes

  • Improved comments regarding HISAT2 for bcbio.
  • Reorganized interactive and non-interactive script handling in system/.
  • Hardened shell scripts using set -Eeuo pipefail.

koopa 0.2.0 (2018-09-23)

Now exporting new scripts in bin/, accessible in $PATH.

Major changes

  • Reworked to be exported in bin/ as simply koopa.
  • Reorganized activation scripts. Split out aliases into Improved automatic activation scripts for HPC and PATH exports.
  • Improved activation handling in
  • Added new info box utility script.
  • Added program list utility.

Minor changes

  • Reorganized activation script for login / non-login and interactive / non-interactive shells.

koopa 0.1.2 (2018-09-05)

  • Improved automatic configuration for bcbio on Harvard HPC clusters.
  • Improved GENCODE workflow scripts.
  • Improved automatic conda configuration.

koopa 0.1.1 (2018-09-05)

  • Now exporting KOOPA_VERSION and KOOPA_DATE global variables.
  • Updated installation instructions.
  • Removed /setup/ config files.
  • Added support for automatic SSH key import, using $SSH_KEY variable.
  • Removed "g*" aliases for GitHub commands (e.g. ga, gc, gd). Too confusing.
  • Simplified the separator bar for koopa message, avoiding unicode.
  • Renamed bcl2fastq_indrop script to bcl2fastq_indrops.
  • Added some utility scripts from macOS bash repo: - delete_fs_cruft - git_pull_all - gzip_dir - install_tex - move_files_up_1_level - rename_from_csv - reset_permissions

koopa 0.1.0 (2018-08-24)

  • Initial stable release.
  • Repo was previously named "seqcloud".
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