kubexec 0.6.1

Execute commands and scripts on Kubernetes pods with Docker access

kubexec

Execute commands and scripts on Kubernetes pods with Docker access.

Designed for use in CLIMB Notebooks.

Installation

pip install -e .

Usage

kubexec [-h] [-d DOCKER_IMAGE] [-n NAMESPACE] [-p POD_NAME] 
        [-m MEMORY] [-c CPU] [-w WORKDIR] [-v VOLUME_MOUNT]
        [--config CONFIG] [--context CONTEXT] [--create-pod]
        [--cleanup] [--verbose] [--dry-run] TARGET

Examples

# Run a simple command
kubexec 'echo "Hello, Kubernetes!"'

# Use specific Docker image
kubexec -d python:3.9 'python -c "import sys; print(sys.version)"'

# Run with resource limits
kubexec -m 4Gi -c 2 'stress --cpu 2 --timeout 60s'

# Execute script file
kubexec ./my_script.sh

# Use existing pod
kubexec -p my-existing-pod 'ls -la'

# Volume mounting
kubexec -v /host/data:/pod/data 'ls /pod/data'

# Save output to local files (works like local commands)
kubexec "ls -la > output.txt"

# Bioinformatics example with SPAdes genome assembler
# This will create spades-out/ directory in your current working directory
kubexec -d community.wave.seqera.io/library/spades:4.1.0--77799c52e1d1054a \
    "spades.py -1 tests/reads/s_6_1.fastq.gz -2 tests/reads/s_6_2.fastq.gz -o spades-out"