Tool Shed: sharing Galaxy tools

Contributors

Authors: Anthony Bretaudeau Loraine Guéguen Stéphanie Legras Bérénice Batut

Questions

• What is a Tool Shed?

• How to install tools and workflows from a Tool Shed into a Galaxy instance?

• What are the Tool Shed repository types?

• How to publish with Planemo?

Objectives

• Discover what is a Tool Shed

• Be able to install tools and workflows from a Tool Shed into a Galaxy instance

• Be able to publish tools with Planemo

1. What is a Tool Shed?

= Galaxy App Store

= Galaxy App Store

• Galaxy tools
• Recipes for installing and compiling tools,
• Data Managers,
• Custom datatypes,
• Exported workflows.

= Galaxy App Store

• For Galaxy administrators, facilitates:
  • installing/updating tools
• For tool developers, facilitates:
  • sharing of Galaxy utilities
  • versioning

Available Tool Sheds

• Galaxy community Tool Shed -> Main Tool Shed
• Galaxy community test Tool Shed -> Sandbox for testing
• List of public Tool Sheds

Tool Shed interface

Example of tool

2. Installing tools from a Tool Shed

Connect your Galaxy to a Tool Shed

• Only for third party toolsheds (Main and Test by default)
• Add <tool_shed /> block in config/tool_sheds_conf.xml
• Restart Galaxy

Install a tool from the Tool Shed

• Go to the admin interface and click on “Search Tool Shed”
• Select a Tool Shed

Install a tool from the Tool Shed

• Search your tool

Install a tool from the Tool Shed

• Types of repository</span>
  • Tools ($name)
  • Tool suites (suite_$name)
  • Tool dependencies (package_$name_$version) (gradually removed, replaced by Conda dependencies)

Install a tool from the Tool Shed

• Install the tool

Install a tool from the Tool Shed

• Install the tool
• Selecting Tool Shed AND conda will make Galaxy to install both
• Recommended: use conda

Install a tool from the Tool Shed

• Check

Manage installed tools

• Admin > Manage installed tools

Manage installed tools

• Click on the name of a tool
• Manage and browse the repository

Tips: How to install workflows

How to install a workflow?

• Admin > Search Tool Shed
• Search the workflow
  1. 
  2. 
• Tools can come with the workflow if they are not yet installed

How to install a workflow?

• No workflow?

How to install a workflow?

• Click on the imported workflow

How to install a workflow?

• Click on the workflow at the bottom of the “Contents of this repository” section

How to install a workflow?

• Repository Actions > Import workflow to Galaxy

How to install a workflow?

• Done!

3. Tool Shed repository types

3.1 Tool with dependencies

Tool with dependencies

3.2 Tool suite

Group of related repositories

Tool suite

• Works but no way to install a single tool

Tool suite

• One repository per individual tool
• A special ‘Tool suite’ repository listing the individual repositories

Tool suite

• relationship between a dependent repository and one or more required repository (tools, datatypes, workflows,…)
• -> One XML file ```xml <?xml version=”1.0”?>

No need to write it yourself, Planemo does it for you

---

###  Tool suite

![phylogeny suite gets uploaded to the TS](../../images/toolsuite3.png)

---

### 3.3 Workflow

---


###  Workflow
![the four tools from the phylogeny pipeline are connected as a workflow](../../images/workflow.png)
- A succession of tools to perform a complete analysis

---

###  Workflow

- In galaxy

![same workflow with galaxy ui](../../images/galaxyWorkflowEx.png)

---

###  Workflow

![extract workflow menu from galaxy](../../images/shareWorkflow.png)

- You get a file: Galaxy-Workflow-NAME.ga

---

###  Workflow

- You have your file Galaxy-Workflow-NAME.ga
- How to automatically install the tools used in the workflow?
  - -> `repository_dependencies.xml`
```xml
<?xml version="1.0"?>
<repositories description="Phylogeny workflow">
   <repository name="suite_phylogeny" owner="galaxy" />
</repositories>

Workflow

Workflow

• Everything must be on the same toolshed

Tips

What about tools working with *.loc files or new datatypes

Tools with *.loc files or new datatypes

• add them to the Tool Shed repository.
• *.loc files and datatypes files should be provided as *.sample file in a tool-data directory.
• tool-data/*.loc.sample files come along with tool_data_table_conf.xml.sample.

Their content or the file themselves are put to the right location on tool set up.

Tools with *.loc files or new datatypes

tool_data_table_conf.xml.sample

<tables>
	<!-- Locations of indexes in the Bowtie2 mapper format -->
	<table name="bowtie2_indexes" comment_char="#">
		<columns>value, dbkey, name, path</columns>
		<file path="tool-data/bowtie2_indices.loc" />
	</table>
</tables>

On install, the content of the file and the right path to the *.loc file is added to shed_tool_data_table_conf.xml

4. Publishing with Planemo

warning There are automated ways to publish to a ToolShed using GitHub and Continuous Integration

Check out these slides, “Publishing tools” section

Configure the target Tool Shed

planemo config_init

• Creates .planemo.yml file in your home directory:

## Planemo Global Configuration File.
## Everything in this file is completely optional - these values can all be
## configured via command line options for the corresponding commands.
## [...]
sheds:
     toolshed:
           #key: "<TODO>"
           #email: "<TODO>"
           #password: "<TODO>"
     testtoolshed:
           #key: "<TODO>"
           #email: "<TODO>"
           #password: "<TODO>"
     local:
           #key: "<TODO>"
           #email: "<TODO>"
           #password: "<TODO>"

Configure the target Tool Shed

• Add your Tool Shed API key in .planemo.yml

## Planemo Global Configuration File.
## Everything in this file is completely optional - these values can all be
## configured via command line options for the corresponding commands.
## [...]
sheds:
     toolshed:
           key: "xxxxxxxxxmytoolshedAPIkeyxxxxxxx"
           #email: "<TODO>"
           #password: "<TODO>"
     testtoolshed:
           #key: "<TODO>"
           #email: "<TODO>"
           #password: "<TODO>"
     local:
           #key: "<TODO>"
           #email: "<TODO>"
           #password: "<TODO>"

Configure repository

planemo shed_init --name="tandem_repeats_finder_2"
                     --owner="gandres"
                     --description="Tandem Repeats Finder description"
                     --long_description="A long long description."
                     --category="Sequence Analysis"
                     [--remote_repository_url=<URL to .shed.yml on github>]
                     [--homepage_url=<Homepage for tool.>]

• Creates .shed.yml file in the current repository (tool repository):

categories: [Sequence Analysis]
description: Tandem Repeats Finder description
long_description: A long long description.
<span id="tandem_repeats_finder_2"><i class="fas fa-link" aria-hidden="true"></i> tandem_repeats_finder_2</span>
owner: gandres

Configure repository

Naming conventions

</small> Planemo will determine the repository type based on these conventions

Configure repository

• Tools and tool suite .shed.yml: implicitly define repositories for each individual tool in the directory and build a suite for those tools.

• Example: trinity/.shed.yml

[...]
auto_tool_repositories:
    name_template: ""
    description_template: " (from the Trinity tool suite)"
suite:
    name: "suite_trinity"
    description: Trinity tools to assemble transcript sequences from Illumina RNA-Seq data.

Check

planemo shed_lint --tools

Linting repository […]/tandem_repeats_finder
Applying linter expansion... CHECK
.. INFO: Included files all found.
Applying linter tool_dependencies_xsd... CHECK
.. INFO: tool_dependencies.xml found and appears to be valid XML
Applying linter tool_dependencies_actions... CHECK
.. INFO: Parsed tool dependencies.
Applying linter repository_dependencies... CHECK
.. INFO: No repository_dependencies.xml, skipping.
Applying linter shed_yaml... CHECK
.. INFO: .shed.yml found and appears to be valid YAML.
Applying linter readme... CHECK
.. INFO: No README found skipping.
+Linting tool […]/tandem_repeats_finder/tandem_repeats_finder_wrapper.xml
[…]

Create repository

planemo shed_create --shed_target testtoolshed

• Don’t forget –shed_target. Default is main toolshed

Create repository

planemo shed_create --shed_target testtoolshed

Repository created
cd '[…]/tandem_repeats_finder' && git rev-parse HEAD
Repository tandem_repeats_finder_2 updated successfully.

Update repository

planemo shed_diff --shed_target testtoolshed

wget -q --recursive -O - 'https://testtoolshed.g2.bx.psu.edu/repository/download?repository_id=6306166e4da9a8bf&changeset_revision=default&file_type=gz' | tar -xzf - -C /tmp/tool_shed_diff_DMcOrR/_testtoolshed_ --strip-components 1
mkdir "/tmp/tool_shed_diff_DMcOrR/_local_"; tar -xzf "/tmp/tmp5ousfg" -C "/tmp/tool_shed_diff_DMcOrR/_local_"; rm -rf /tmp/tmp5ousfg
cd "/tmp/tool_shed_diff_DMcOrR"; diff -r _local_ _testtoolshed_
diff -r _local_/tandem_repeats_finder.xml _testtoolshed_/tandem_repeats_finder.xml
41d40
<     <param name="fileout_label2" type="text" value="Unused" label="none" help="Output name for files" />

• The repository needs to be updated

Update repository

planemo shed_update --check_diff --shed_target testtoolshed

wget -q --recursive -O - 'https://testtoolshed.g2.bx.psu.edu/repository/download?repository_id=6306166e4da9a8bf&changeset_revision=default&file_type=gz' | tar -xzf - -C /tmp/tool_shed_diff_DMcOrR/_testtoolshed_ --strip-components 1
mkdir "/tmp/tool_shed_diff_DMcOrR/_local_"; tar -xzf "/tmp/tmp5ousfg" -C "/tmp/tool_shed_diff_DMcOrR/_local_"; rm -rf /tmp/tmp5ousfg
cd "/tmp/tool_shed_diff_DMcOrR"; diff -r _local_ _testtoolshed_
diff -r _local_/tandem_repeats_finder.xml _testtoolshed_/tandem_repeats_finder.xml
41d40
<     <param name="fileout_label2" type="text" value="Unused" label="none" help="Output name for files" />
Repository tandem_repeats_finder updated successfully.
Repository metadata updated.

• The repository has been updated

Update repository

planemo shed_update --check_diff --shed_target testtoolshed

• The repository has been updated

Publishing to the Tool Shed

Command-line utilities to assist in building and publishing Galaxy tools.

Checklist (3/3)

• Initiate the .shed.yml file with

  planemo shed_init
  

• Create the repository on ToolShed with

  planemo shed_create
  

• Install and test the wrapper on a Galaxy instance
• Improve the wrapper and push modification on toolshed

  planemo shed_update
  

References

• ToolShed
• Install tools from the ToolShed
• Publish tools with Planemo

Hands-on

The goal

Publish your tool (seqtk_seq) in your local toolshed with Planemo

Step 1: Start and configure your toolshed

• Start your toolshed (in galaxy home directory):

  ./run_tool_shed.sh
  

• Toolshed available at http://localhost:9009

Step 2: Use planemo to publish your tool

Step 2: Use planemo to publish your tool

planemo config_init

• Creates file .planemo.yml in your home directory.

[...]  local:
#key: "<TODO>"
email: "galaxy@localhost.fr"
password: "azerty"

planemo shed_init --name=seqtk_seq --owner=galaxy --description="common transformation of FASTA/Q" --category="Fasta Manipulation"

planemo shed_lint .

planemo shed_create --shed_target local

Step 3: Update your tool and then use planemo to update your tool on the Tool Shed

Step 3: Update your tool and then use planemo to update your tool on the Tool Shed

planemo shed_diff --shed_target local

planemo shed_update --check_diff --shed_target local

Key Points

• Use Planemo
• Contribute to the Main Tool Shed

Thank you!