koopa 0.5.6 (2019-09-18)
gencode-gtfPython scripts for downloaded GENCODE genome annotations. Currently supports Homo sapiens and Mus musculus.
link-msigdb: Shared MSigDB file annotation utility.
- 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)
- Updater now checks for: oh-my-zsh, spacemacs symlinks in config directory.
- Added install support for ChromHMM.
- Bug fix for directory creation in Python cellar script.
- ZSH configuration improvements.
koopa 0.5.4 (2019-09-05)
- 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)
- Improved zsh activation and oh-my-zsh configuration handling when koopa is
/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.
- 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
koopafunction. Instead, these are now called more consistently using internal prefixes. (e.g.
koopa 0.5.1 (2019-08-15)
- Bug fixes for koopa activation inside a subshell (e.g. tmux or slurm queue).
koopa 0.5.0 (2019-08-14)
- 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
--dotfilesflag or can use
install-dotfilesscript after installation.
- Fixed shell configuration when
koopa 0.4.6 (2019-08-01)
ftp-mirror: Script that helps quickly mirror an FTP directory using wget.
install-rcheck: Utility for quickly checking R packages.
- Reworked the file paths of some dot files related to vim and zsh config.
- 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)
- Improved detection and handling of unbound variables during installation and activation of koopa.
koopa 0.4.4 (2019-07-28)
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.
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.
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.
- Installation will now clone private scripts and docker recipes. The activation
script now knows to look for these and will add
- 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)
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)
- Improved automatic XDG configuration in
~/.config/koopa. Needed to update configuration of R symlink.
koopa 0.4.1 (2019-07-11)
- Removed support for ksh. This shell does not support usage of
localvariables 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.
- Harden scripts to pass shellcheck.
- Switch back to using
! -zconsistently 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
copy-bam-filesutility, which makes it easier to quickly set up an IGV session, which requires both
*.bam.baifiles. Previously, this was named
koopa 0.4.0 (2019-06-13)
This is the first release supported to work when installed at
This enables shared shell configuratino of all users, via configuration in
/etc/profile.d/) instead of relying on
- koopa now checks for root and doesn't attempt to activate.
- Improved dotfile initialization, and no files are overwritten by default.
installscript, and added usage accessible via
- Reworked activation scripts to support multi-user config.
- Reworked shared script header approach.
- Improved automatic
KOOPA_HOMEpath 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)
- Improved update script.
- Install koopa using simply
- Improved attempt at dotfiles auto-linking during
- Improved OS-specific PATH exports.
- Switched to using
KOOPA_TMP_DIRvariables for build scripts.
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-systemscripts for supported operating systems.
- 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
set +xfor some scripts, which was used for testing.
- Renamed pre-flight check scripts.
- Hardened zsh setup scripts, using
- 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.
- koopa now clones Mike's dotfiles repo as a submodule, in
- Moved install scripts from
install/into nested inside
- Reorganized exported scripts in
- Improved platform checks and related messages.
sudo-*scripts into nested
sudo/directory, to allow conditional access in
$PATHexport for sudo users only.
check-versionsscript to determine if R is installed. Added additional improvements to the R code for these checks.
rsync-azure-files: Now excluding
work/directories, for bcbio.
- Initial setup of sudo scripts for RHEL 7.
- Improved information shown in
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-dl-related utility scripts.
- Added support files for fedora
etc/ld.so.conf.d/. 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-versionsprogram, for additional version checks.
- Improved build scripts in
/tmp/for temp files.
- New build scripts: bash, coreutils, gnupg, openssl, pass, r, rstudio-server, and zsh.
- Now using a shared
__init__.shscript 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.
shellcheck-recursiveto check for shell shebang, rather than relying on the file extension.
download-gtfin 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.
- 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
activate.shscript 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
- 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
- Reorganized installer scripts exported in
bin/including conda scripts,
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.
rsync-azure-files.shscript for working with Azure Shares (Samba).
- Reorganized other scripts accessible via
- 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
- Conda now will only activate when
CONDA_DEFAULT_ENVis 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)
- Reworked activation script to use POSIX instead of bash conventions. Notably,
this involves switching to
- Early return using
exitwhen koopa is already active, to prevent accidental lockout on a remote SSH connection.
- Improved support for ZSH in activation script.
- Initial commit of
- Now checking on Travis CI only against master branch.
koopa 0.2.3 (2019-01-01)
- Improved variable quoting inside
- Reworked activation steps in main
- Deleted function scripts inside
functions/. Rethinking this approach.
koopa 0.2.2 (2018-12-19)
trashutility, which moves files to
~/.Trash, similar to macOS.
sudo_install_r_cran. Rethinking this approach in a future update.
- Removed these macOS-specific scripts:
- Improved error message for unsupported shells in
koopa 0.2.1 (2018-11-24)
git_status_all, corresponding to
- Improved comments regarding HISAT2 for bcbio.
- Reorganized interactive and non-interactive script handling in
- Hardened shell scripts using
set -Eeuo pipefail.
koopa 0.2.0 (2018-09-23)
Now exporting new scripts in
bin/, accessible in
koopa.shto be exported in
- Reorganized activation scripts. Split out aliases into
01_aliases.sh. Improved automatic activation scripts for HPC and PATH exports.
- Improved activation handling in
- Added new
info.shinfo box utility script.
list.shprogram list utility.
- 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
- Updated installation instructions.
- Added support for automatic SSH key import, using
- Removed "g*" aliases for GitHub commands (e.g. ga, gc, gd). Too confusing.
- Simplified the separator bar for koopa message, avoiding unicode.
- 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".