ShedTool

This document provides full set of instructions how to place a package into ShedTool in galaxy server.

Install and/or activate planemo

Based on this instructions: /home/rv43/planemo.readme

Activate environment:

. planemo/bin/activate

Install planemo:

python3 -m venv planemo
. planemo/bin/activate
pip install planemo

As needed:

pip install --upgrade pip
pip install -U planemo (to update planemo)

Next, we need to create .shed.yml file Create a .shed.yml with the right credentials and make the name in there the same as in the repo, see instructions here. Please note:

  • for type use: unrestricted

  • and choose one of the categories this repo

Registion step

To use our shed tool we need to register at https://testtoolshed.g2.bx.psu.edu and get the API key.

Shed tool

Create a new tool with planemo:

  • create your shed tool xml file, e.g. chap.xml

  • planemo shed_create --shed_target testtoolshed --shed_key <API key> get the API key from user prefferences in the testtoolshed

  • or update existing shed tool:

planemo shed_update --check_diff --shed_target testtoolshed --shed_key <API key>

Optionally, we may check a tool XML file for common problems:

planemo lint [tool.xml]
planemo test [tool.xml]
```
Check https://testtoolshed.g2.bx.psu.edu/ for your tool, e.g.
search for your tool name and you should see:
```
Tool id and version      Repository name↓           Owner       Revision
chapmlaas: 0.1.0+galaxy0 package_chapmlaas_0_0_2    vkuznet     0:5ec75e142574 (2023-04-05)
```

### Upload tool to galaxy-dev
To install the tool on galaxy-dev:
1. Login as an administrator to https://galaxy-dev.classe.cornell.edu
2. Go to the "Admin" tab at the top of the page
3. In the sidebar on the left, go to "Install and uninstall" (admin->Tool
Management->Install and Uninstall)
4. Search for your testtoolshed tool
5. Click "Install"
6. Select a target section (e.g. X-IMG) and click "OK"

### Manual procedure
If the testtoolshed does not show up, in config/galaxy.yml add:
```
    tool_sheds_config_file: /nfs/chess/galaxy-dev/server/config/tool_sheds_conf.xml
```
then create:
```
/nfs/chess/galaxy-dev/server/config/tool_sheds_conf.xml
```
with:
```
<?xml version="1.0"?>
<tool_sheds>
    <tool_shed name="Galaxy Main Tool Shed" url="https://toolshed.g2.bx.psu.edu/"/>
    <!-- Test Tool Shed should be used only for testing purposes. -->
    <tool_shed name="Galaxy Test Tool Shed" url="https://testtoolshed.g2.bx.psu.edu/"/>
</tool_sheds>
```