Thanks a lot, Marius!

I am a newbie to this complex system and want a quick clone/install locally. I have spent over two weeks on the process. There are many configuration files and environment variables or dependencies to sort out. I wish the sample configuration files would include most of the options so that new installation just needs to comment out or delete unwanted ones.

Anyway, here is the error I got:

[galaxy@Pegasus ansible-galaxy-tools]$ python files/install_tool_shed_tools.py -h
Traceback (most recent call last):
  File "files/install_tool_shed_tools.py", line 49, in <module>
    logging.captureWarnings(True)  # Capture HTTPS warngings from urllib3
AttributeError: 'module' object has no attribute 'captureWarnings'

If I run this after activating the galaxy_env and install ensible, bioblend, argparse and importlib, the same error came up. I guess this is Python 2.6 issue. Any solutions known?

Thanks,

Bill

---

From: Marius van den Beek <m.vandenbeek@gmail.com>
Sent: Friday, March 4, 2016 11:03 AM
To: William Ge
Cc: Dannon Baker; galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

 

The list of tools installed on usegalaxy.org is conviniently desposited here:

Galaxy usegalaxy.org The Galaxy analysis interface requires a browser with Javascript enabled. Please enable Javascript and refresh this page. Galaxy. Javascript Required for Galaxy

https://github.com/galaxyproject/usegalaxy-playbook/blob/master/files/galaxy/usegalaxy.org/tool_list.yaml

Normally you should be able to use this command outlined above to get all the tools that usegalaxy.org has,

including the dependencies.

PS. please keep all traffic on the mailing list

On 4 March 2016 at 19:59, Marius van den Beek <m.vandenbeek@gmail.com> wrote:

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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