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(a)gmail.com>
Sent: Friday, March 4, 2016 11:03 AM
To: William Ge
Cc: Dannon Baker; galaxy-dev(a)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<http://usegalaxy.org/> is conviniently
desposited here:
Galaxy<http://usegalaxy.org/>
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/gal...
Normally you should be able to use this command outlined above to get all the tools that
usegalaxy.org<http://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<mailto: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/t...
Cheers,
Marius
On 4 March 2016 at 19:11, William Ge
<wge@centrilliontech.com<mailto: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<mailto:m.vandenbeek@gmail.com>>
Sent: Friday, March 4, 2016 7:25 AM
To: Dannon Baker
Cc: William Ge;
galaxy-dev@lists.galaxyproject.org<mailto: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
[
https://avatars0.githubusercontent.com/u/338642?v=3&s=400]<https:/...
afgane/galaxy-tools-playbook ·
GitHub<https://github.com/afgane/galaxy-tools-playbook>
github.com<http://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/i...
if you're more comfortable not using ansible.
Cheers,
Marius
On 4 March 2016 at 13:43, Dannon Baker
<dannon.baker@gmail.com<mailto: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<mailto: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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___________________________________________________________
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and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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