Extras

Overview

This section entails

• ica-illumination
• ica-make-md5sum
• gds-diskusage
• ica-get-tasks-from-workflow-history
• ica-fastq-gzip-to-ora
• ica-get-task-pod-metrics

ica-illumination

auto-completion: ✅

Launch illumination in a given project context.
This will require you to have added the 'read-only' token to a given project with ica-add-access-token.

Options:

• --project-name
• --port

Requirements:

• docker
• jq

Environment Variables:

• BROWSER

ica-make-md5sum

auto-completion: ✅

Generates a md5sum with .md5sum prefix adjacent to a GDS file

Options:

• --gds-path
• --log-path

Requirements:

• curl
• jq

Environment Variables:

• ICA_ACCESS_TOKEN

GIF 🚧

gds-diskusage

auto-completion: ✅

Given a directory, create an interactive diskusage map with xdiskusage

Options:

• --gds-path

Requirements:

• curl
• jq
• python3
• xdiskusage

Environment Variables:

• ICA_BASE_URL
• ICA_ACCESS_TOKEN

GIF 🚧

ica-get-tasks-from-workflow-history

auto-completion: ✅

Given an ica workflow run id, collects all tasks executed by this workflow by traversing the workflow history

Options:

• --ica-workflow-run-id

Requirements:

• curl
• jq

Environment Variables:

• ICA_BASE_URL
• ICA_ACCESS_TOKEN

ica-fastq-gzip-to-ora

auto-completion: ✅

Given an input directory of fastqs that is an output directory of a bclconvert run, convert to ora and place ora files in the output directory

Options:

• --input-path
• --output-path
• --ora-reference-path
• --compression-type

Requirements:

• curl
• jq
• python3

Environment Variables:

• ICA_BASE_URL
• ICA_ACCESS_TOKEN

ica-get-task-pod-metrics

auto-completion: ✅

Given a task id as input collect the max and average cpu / memory usage of that task

Options:

• --ica-task-run-id

Requirements:

• curl
• jq
• python3

Environment Variables:

• ICA_BASE_URL
• ICA_ACCESS_TOKEN

ica-plot-tasks-pod-metrics

auto-completion: ✅

Given a task id as input collect the max and average cpu / memory usage of that task

Options:

• --ica-tasks-list
• --output-prefix
• --title-prefix

Requirements:

• curl
• jq
• python3

Environment Variables:

• ICA_BASE_URL
• ICA_ACCESS_TOKEN