Question: How to find exact tool revision
1
gravatar for Mic
3.0 years ago by
Mic70
Australia
Mic70 wrote:

Hello,

This link https://usegalaxy.org/api/tools provide me with the following information:

    {
    [
    ...
            {
                "description": "", 
                "id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0", 
                "link": "/tool_runner?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fdevteam%2Fpicard%2FrgPicardMarkDups%2F1.56.0", 
                "min_width": -1, 
                "model_class": "Tool", 
                "name": "Mark Duplicate reads", 
                "panel_section_id": "picard_beta", 
                "panel_section_name": "NGS: Picard (beta)", 
                "target": "galaxy_main", 
                "version": "1.56.0"
            }
    ...
        ], 
        "id": "picard_beta", 
        "model_class": "ToolSection", 
        "name": "NGS: Picard (beta)", 
        "version": ""
    }

How can I find out what revision number Picard version 1.56.0 is so I could use this script (/galaxy/scripts/api/install_tool_shed_repositories.py)?

Thank you in advance.

Mic

 

galaxy docker • 638 views
ADD COMMENTlink modified 3.0 years ago by Jennifer Hillman Jackson25k • written 3.0 years ago by Mic70
1
gravatar for Martin Čech
3.0 years ago by
Martin Čech ♦♦ 4.9k
United States
Martin Čech ♦♦ 4.9k wrote:

That is a very good question. Sadly the API does not return this information.

The Main's configuration files are public here: https://github.com/galaxyproject/usegalaxy-playbook/tree/master/files/galaxy/usegalaxy.org/var and the exact picard revision is visible here: https://github.com/galaxyproject/usegalaxy-playbook/blob/master/files/galaxy/usegalaxy.org/var/migrated_tools_conf.xml#L627

I filled an issue requesting this the API enhancement here: https://github.com/galaxyproject/galaxy/issues/982

ADD COMMENTlink written 3.0 years ago by Martin Čech ♦♦ 4.9k
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