koopa app¶
aws¶
AWS utilities (Batch, EC2, ECR, S3).
app aws batch fetch-and-run¶
Submit an AWS Batch fetch-and-run job.
--queue--job-definition--job-name--vcpus--memory--profile
app aws batch list-jobs¶
List AWS Batch jobs in a queue.
--queue--status--profile
app aws ec2 instance-id¶
Print the current EC2 instance ID.
app aws ec2 list-running-instances¶
List running EC2 instances.
--profile
app aws ec2 map-instance-ids-to-names¶
Map EC2 instance IDs to Name tags.
--profile
app aws ec2 stop¶
Stop EC2 instances.
--profile
app aws ecr login-private¶
Authenticate Docker to a private ECR registry.
--region--account-id--profile
app aws ecr login-public¶
Authenticate Docker to the public ECR gallery.
--region
app aws s3 delete-versioned-glacier-objects¶
Delete versioned Glacier objects from an S3 bucket.
--bucket--prefix--profile
app aws s3 delete-versioned-objects¶
Delete versioned objects from an S3 bucket.
--bucket--prefix--profile
app aws s3 dot-clean¶
Remove macOS dot-files from an S3 path.
--dryrun--profile
app aws s3 find¶
Find S3 keys matching a pattern under a prefix.
--bucket--prefix--pattern--profile
app aws s3 list-large-files¶
List S3 objects above a size threshold.
--bucket--min-size-mb--prefix--profile
app aws s3 ls¶
List an S3 path.
--recursive--profile
app aws s3 mv-to-parent¶
Move S3 objects up one directory level.
--dryrun--profile
app aws s3 sync¶
Sync files between local and S3, or between S3 buckets.
--delete--dryrun--exclude--include--profile
app aws s3 sync-git-repo¶
Sync a local git repo to S3, respecting .gitignore.
--delete--dryrun--profile
bioconda¶
bioconda-recipes maintenance utilities.
app bioconda autobump-recipe¶
Check out a bioconda-recipes autobump PR branch for review.
bowtie2¶
Bowtie 2 short-read aligner wrappers.
app bowtie2 align paired-end¶
Align paired-end reads with Bowtie 2.
--index-dir--fastq-dir--output-dir--output-format--reference-fasta
app bowtie2 index¶
Build a Bowtie 2 genome index.
--genome-fasta-file--output-dir
brew¶
Homebrew maintenance utilities.
app brew cleanup¶
Run ‘brew cleanup’.
app brew dump-brewfile¶
Dump the current Homebrew Bundle to a Brewfile.
app brew install-bundle¶
Install packages from a Brewfile via ‘brew bundle’.
app brew outdated¶
List outdated Homebrew packages.
app brew reset-core-repo¶
Reset the homebrew/core git repo to match its remote.
app brew reset-permissions¶
Reset ownership and permissions on the Homebrew prefix.
app brew uninstall-all-brews¶
Uninstall all Homebrew-managed packages.
app brew upgrade¶
Upgrade all Homebrew packages.
app brew version¶
Print the installed Homebrew version.
claude¶
Claude Code configuration maintenance utilities.
app claude archive-plans¶
Archive old Claude Code plan files into date-based subdirectories.
--days--dry-run
app claude audit-tokens¶
Report approximate token cost of Claude config files.
--max-tokens--scope--project-dir
conda¶
conda environment management utilities.
app conda clean-cache¶
Clean the conda package cache.
app conda create-env¶
Create a conda environment from packages or an environment file.
--file--prefix--force--latest
app conda remove-env¶
Remove a conda environment.
current¶
Query the current upstream version of a package or resource.
app current aws-cli-version¶
Print the current upstream AWS CLI version.
app current bioconductor-version¶
Print the current Bioconductor release version.
app current conda-package-version¶
Print the current version of a conda package.
app current ensembl-version¶
Print the current Ensembl release version.
app current flybase-version¶
Print the current FlyBase release version.
app current gencode-version¶
Print the current GENCODE release version.
app current git-version¶
Print the current upstream Git version.
app current github-release-version¶
Print the latest GitHub release version for a repo.
app current github-tag-version¶
Print the latest GitHub tag version for a repo.
app current gnu-ftp-version¶
Print the current version of a GNU FTP-hosted package.
app current google-cloud-sdk-version¶
Print the current upstream Google Cloud SDK version.
app current latch-version¶
Print the current Latch SDK version.
app current pypi-package-version¶
Print the current version of a PyPI package.
app current python-version¶
Print the current upstream Python version.
app current refseq-version¶
Print the current RefSeq release version.
app current wormbase-version¶
Print the current WormBase release version.
docker¶
Docker image build, run, and cleanup utilities.
app docker build¶
Build a Docker image for local and/or remote platforms.
--local--remote--memory--no-push
app docker prune-all-images¶
Remove all local Docker images.
app docker prune-old-images¶
Remove old, unused local Docker images.
app docker remove¶
Remove Docker images matching a pattern.
app docker run¶
Run a Docker image, with platform and bind-mount shortcuts.
--arm--x86--bash--bind
file¶
File compression and renaming utilities.
app file compress¶
Compress a file or directory into a tar.gz archive.
--output
app file convert-line-endings¶
Convert CRLF line endings to LF in place.
app file rename-to-lowercase-ext¶
Rename file extensions to lowercase.
ftp¶
FTP mirroring utilities.
app ftp mirror¶
Mirror an FTP site with wget.
--host--user--dir
git¶
Git repository maintenance utilities.
app git pull¶
Pull the latest changes in a git repo.
app git push-submodules¶
Push all git submodules in a repo.
app git rename-master-to-main¶
Rename a repo’s master branch to main.
app git reset¶
Hard-reset a git repo to its upstream branch.
app git reset-fork-to-upstream¶
Reset a forked repo to match its upstream.
app git rm-submodule¶
Remove a git submodule.
app git rm-untracked¶
Remove untracked files from a git repo.
gpg¶
GnuPG agent management utilities.
app gpg prompt¶
Prompt for the GPG passphrase to unlock the agent.
app gpg reload¶
Reload the GPG agent.
app gpg restart¶
Restart the GPG agent.
hisat2¶
HISAT2 spliced aligner wrappers.
app hisat2 align paired-end¶
Align paired-end reads with HISAT2.
--index-dir--fastq-dir--output-dir--gtf-file
app hisat2 align single-end¶
Align single-end reads with HISAT2.
--index-dir--fastq-dir--output-dir--gtf-file
app hisat2 index¶
Build a HISAT2 genome index.
--genome-fasta-file--output-dir--gtf-file
jekyll¶
Jekyll static site build and deploy utilities.
app jekyll deploy-to-aws¶
Build a Jekyll site and deploy it to S3 + CloudFront.
--bucket--distribution-id--profile--local-prefix
app jekyll serve¶
Serve a Jekyll site locally for development.
kallisto¶
kallisto pseudo-alignment wrappers.
app kallisto index¶
Build a kallisto transcriptome index.
--transcriptome-fasta-file--output-dir
app kallisto quant paired-end¶
Quantify paired-end reads with kallisto.
--index-dir--fastq-dir--output-dir
app kallisto quant single-end¶
Quantify single-end reads with kallisto.
--index-dir--fastq-dir--output-dir
koopa¶
koopa.acidgenomics.com Sphinx docs site publishing.
app koopa prune-stale-docs¶
Remove stale S3 keys left over from a previous docs build.
--no-dryrun
app koopa publish-docs¶
Build and publish the koopa Sphinx docs site to koopa.acidgenomics.com.
--no-invalidate--dryrun
md5sum¶
md5sum checksum utilities.
app md5sum check-to-new-md5-file¶
Compute md5sum checksums and log them to a new .md5 file.
miso¶
MISO alternative-splicing index utilities.
app miso index¶
Build a MISO alternative-splicing index.
--gff-file--output-dir
photos¶
Photo and video file renaming utilities.
app photos rename-with-exiftool¶
Rename photos and videos by capture date using exiftool.
python¶
python.acidgenomics.com package index and docs publishing.
app python publish¶
Build and publish a Python package to python.acidgenomics.com.
app python publish-docs¶
Build and publish a package’s Sphinx docs to python.acidgenomics.com.
app python reindex¶
Regenerate the PEP 503 index and landing page for python.acidgenomics.com.
app python sync-docs-theme¶
Sync koopa’s shared Sphinx theme into one or more doc trees.
--check
r¶
r.acidgenomics.com R package repository publishing.
app r archive¶
Archive stale R package source tarballs.
--no-invalidate
app r bioconda-check¶
Check R package versions against bioconda-recipes.
app r check¶
Run R CMD check on an R package.
app r clean-orphan-binaries¶
Remove orphaned R package binaries with no matching source.
--no-invalidate
app r configure-environ¶
Configure R’s Renviron file.
app r configure-java¶
Configure R’s Java bindings.
app r configure-ldpaths¶
Configure R’s shared library search paths.
app r configure-makevars¶
Configure R’s Makevars build settings.
app r copy-files-into-etc¶
Copy koopa R configuration files into R’s etc/ directory.
app r deploy¶
Deploy the current state of r.acidgenomics.com.
--no-invalidate
app r gfortran-libs¶
Print the gfortran runtime library search path.
app r install-packages-in-site-library¶
Install R packages into the site library.
app r package-version¶
Print the installed version of an R package.
app r paste-to-vector¶
Format items as an R character vector literal.
app r publish¶
Build, check, and publish an R package to r.acidgenomics.com.
--no-check--no-deploy--no-invalidate--no-tag
app r publish-docs¶
Build and publish an R package’s pkgdown docs to r.acidgenomics.com.
--no-invalidate
app r publish-from-github¶
Publish an R package release directly from its GitHub repo.
--org--check--no-invalidate
app r reindex¶
Regenerate the drat index and landing page for r.acidgenomics.com.
--no-invalidate
app r remove-packages-in-system-library¶
Remove non-base packages from R’s system library.
app r script¶
Run an R script with koopa’s R.
app r shiny-run-app¶
Run a Shiny app locally.
--port
app r system-packages-non-base¶
List non-base packages installed in R’s system library.
app r version¶
Print the installed R version.
rnaeditingindexer¶
RNA editing indexer wrapper.
app rnaeditingindexer¶
Run the RNA editing indexer on a directory of BAM files.
--bam-dir--output-dir--genome--example
rsem¶
RSEM transcript quantification wrappers.
app rsem index¶
Build an RSEM reference index.
--genome-fasta-file--output-dir--gtf-file--num-threads
app rsem quant bam¶
Quantify transcript expression from a BAM file with RSEM.
--bam-file--index-dir--output-dir
salmon¶
salmon transcript quantification wrappers.
app salmon detect-fastq-library-type¶
Detect the FASTQ library type using salmon.
--index-dir--r1--r2--threads
app salmon index¶
Build a salmon transcriptome index.
--transcriptome-fasta-file--output-dir
app salmon quant bam¶
Quantify transcript expression from a BAM file with salmon.
--index-dir--fastq-dir--output-dir
app salmon quant paired-end¶
Quantify paired-end reads with salmon.
--index-dir--fastq-dir--output-dir
app salmon quant single-end¶
Quantify single-end reads with salmon.
--index-dir--fastq-dir--output-dir
sra¶
SRA (Sequence Read Archive) download utilities.
app sra download-accession-list¶
Download the accession list for an SRA study.
--srp-id--file
app sra download-run-info-table¶
Download the run info table for an SRA study.
--srp-id--file
app sra fastq-dump¶
Extract FASTQ files from prefetched SRA data.
--prefetch-directory--fastq-directory--no-compress
app sra prefetch¶
Prefetch SRA run data by accession.
--accession-file--output-dir
ssh¶
SSH key generation utilities.
app ssh generate-key¶
Generate one or more SSH key pairs.
--prefix
star¶
STAR spliced aligner wrappers.
app star align paired-end¶
Align paired-end reads with STAR.
--index-dir--fastq-dir--output-dir--gtf-file
app star align single-end¶
Align single-end reads with STAR.
--index-dir--fastq-dir--output-dir--gtf-file
app star index¶
Build a STAR genome index.
--genome-fasta-file--output-dir--gtf-file
sys¶
Low-level system inspection utilities.
app sys linker-info¶
Show shared library dependencies (ldd on Linux, otool -L on macOS).
wget¶
wget recursive mirroring utilities.
app wget recursive¶
Recursively mirror a password-protected site with wget.
--url--user--password