There is no real step by step guide, but the script itself has a help text:

$ python install_tool_shed_tools.py -h

Also make sure you have bioblend installed (pip install bioblend)
It does more things than just installing tools. To just install tools you would use a command line like this:

python install_tool_shed_tools.py -a "your new admin api key" -g "your new galaxy instance url" -t tool_list.yml

tool_list.yml follows the format outlined here:
https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/tool_list.yaml.sample

Cheers,
Marius

On 4 March 2016 at 19:11, William Ge <wge@centrilliontech.com> wrote:

Thank you both, Marius and Dannon!

Since I am not familiar with ansible, I will just run the python script. I am reading about the usage of the script, trying to figure out what configuration needs  to be in place and what options to use. Is there  a step-by-step guide for using this script somewhere?

Best regards,
Bill

---

From: Marius van den Beek <m.vandenbeek@gmail.com>
Sent: Friday, March 4, 2016 7:25 AM
To: Dannon Baker
Cc: William Ge; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

 

Hi Bill,

I think you're trying to use the ansible-galaxy-tools role as a playbook:

This won't work, you can only include the role in your playbook,

or use this playbook https://github.com/afgane/galaxy-tools-playbook

afgane/galaxy-tools-playbook · GitHub github.com README.md A ready-to-use Ansible playbook for the Galaxy Tools role. Before you can use this playbook, you need to install Ansible: $ pip install ansible

You can also directly use the python script in https://github.com/galaxyproject/ansible-galaxy-tools/blob/master/files/install_tool_shed_tools.py

if you're more comfortable not using ansible.

Cheers,

Marius

On 4 March 2016 at 13:43, Dannon Baker <dannon.baker@gmail.com> wrote:

I haven't seen this before but did a little googling.  What version is your ansible installation?   If it's a little bit older, (https://github.com/ansible/ansible/issues/5412) might be what you're seeing.

It's a bit of a long read, but it looks like reinstalling or updating your ansible (or installing a new one in a fresh virtualenv for isolation) should resolve it.

Let me know if that doesn't fix it up for you.

On Thu, Mar 3, 2016 at 10:08 PM, William Ge <wge@centrilliontech.com> wrote:

Hi, all,

 

Sorry to bother you again. I am trying to install tools using the script. I have downloaded the playbook, but stuck here:

 

[galaxy@Pegasus ansible-galaxy-tools]$ ansible-playbook tasks/tools.yml -i "localhost," --extra-vars galaxy_tools_api_key=xcd2Glx

ERROR: pip is not a legal parameter of an Ansible Play

 

I did not find anything related on the Galaxy search either. Any help will be appreciated.

 

The web Admin interface only allows tool installation one by one. I wish it allows batch installation there.

 

Thanks,

Bill

 

 

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