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:
On 4 March 2016 at 19:11, William Ge <wge(a)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?
*From:* Marius van den Beek <m.vandenbeek(a)gmail.com>
*Sent:* Friday, March 4, 2016 7:25 AM
*To:* Dannon Baker
*Cc:* William Ge; galaxy-dev(a)lists.galaxyproject.org
*Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an
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
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
You can also directly use the python script in
if you're more comfortable not using ansible.
On 4 March 2016 at 13:43, Dannon Baker <dannon.baker(a)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, (
) might be what you're
> 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(a)centrilliontech.com>
>> 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.
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> Please keep all replies on the list by using "reply all"
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> and other Galaxy lists, please use the interface at:
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