Galaxy Workflow Validation

Register a Dockstore account

1. Go to https://dockstore.org/register
2. Login with either github or google account

Obtain Dockstore Token

1. Click on your username at the top right
2. Click on *account* on the drop-down menu
3. Get your Token under *Dockstore Account* 

Environment Setup (Ubuntu)

1. Go to https://dockstore.org/quick-start
2. Install Java 17 (This example installs OpenJDK 17)
   sudo apt-get update -q && sudo apt install -y openjdk-17-jdk
3. Install Docker Engine
   sudo usermod -aG docker $USER
   exec newgrp docker
4. Install Dockstore CLI
   mkdir -p ~/dockstore/bin
	curl -L -o ~/bin/dockstore https://github.com/dockstore/dockstore-cli/releases/download/1.18.0/dockstore
	chmod +x ~/bin/dockstore
	echo 'export PATH=~/bin:$PATH' >> ~/.bashrc
	source ~/.bashrc
5. Add dockstore token to .dockstore/config
	mkdir -p ~/.dockstore
	printf "token: token_is_availiable_in_your_account_on_dockstore\nserver-url: https://dockstore.org/api\n" > ~/.dockstore/config

Planemo Setup

Planemo is used to test workflow, tools and etc.

python -m venv planemo
. planemo/bin/activate
pip install planemo

Reference: https://planemo.readthedocs.io/en/stable/installation.html

Bioblend Setup

Bioblend is used to query and retrieve tools information from Toolshed.

pip install bioblend

Dockstore list, search or download workflow

List all iwc published workflows on dockstore

dockstore workflow search --pattern iwc-workflows

Use Dockstore cli to search for particular workflow

dockstore workflow search --pattern Assembly-decontamination-VGP9

The output of the dockstore cli search with pattern parameter

MATCHING WORKFLOWS
---------------------------------------------
NAME                                                          DESCRIPTION   GIT REPO                                                         PUBLISHED
github.com/iwc-workflows/Assembly-decontamination-VGP9/main                 git@github.com:iwc-workflows/Assembly-decontamination-VGP9.git   Yes

Query workflow version

dockstore workflow info --entry github.com/iwc-workflows/Assembly-decontamination-VGP9/main

Get workflow version

bash get_wf_version_arg.sh github.com/iwc-workflows/Assembly-decontamination-VGP9/main

Output
main
v1.3
v1.2
v1.1
v1.0
v0.8
v0.7
v0.6
v0.5
v0.4
v0.3
v0.2
v0.1.6
v0.1.4
v0.1.3
v0.1.2
v0.1.1
v0.1

Dockstore download specific version of a workflow

dockstore workflow download --entry github.com/iwc-workflows/Assembly-decontamination-VGP9/main:v1.3

Note: The Assembly-decontamination-VGP9 (v1.3) workflow on github

Obtain Galaxy API Key

1. Go to https://usegalaxy.org.au/
2. Log into Galaxy
3. Click on your username at the top right
4. Click on *preference*
5. Click on *Manage Galaxy API Key* 

Setup Planemo for testing workflow

planemo profile_create galaxy_profile --galaxy_url https://usegalaxy.org.au --galaxy_user_key your_galaxy_api_key --engine external_galaxy

Test the downloaded galaxy workflow file (ga)

This step generates tool_test_output.json and it can use as a missing tool report

planemo test Scaffolding-HiC-VGP8.ga --profile galaxy_profile

or

planemo test Assembly-decontamination-VGP9.ga --profile galaxy_profile

Check missing tools

Transform the tool_test_output.json format

cat tool_test_output.json | jq -r '
  .tests[0].data.execution_problem |
  capture("(?<tools>toolshed[^\"]*)").tools |
  split(", ")[] '

Run workflow inspector

This workflow inspector contains the dockstore and planemo tool to query and test the workflow of interest

python workflow_inspector.py --entry "github.com/iwc-workflows/Assembly-decontamination-VGP9/main" --version "v1.3"

REFERENCE

• IWC workflow
  • Github repo
  • README
• Running Galaxy workflows
• Workflow Example on Dockstore
  • Assembly-decontamination-VGP9
  • Scaffolding-HiC-VGP8
• Dockstore documentation
• Browsing Workflow in Dockstore and Galaxy
• GTN material
  • workflow automation