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.vandenb...@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<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/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<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.vandenb...@gmail.com<mailto:m.vandenb...@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
<w...@centrilliontech.com<mailto:w...@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.vandenb...@gmail.com<mailto:m.vandenb...@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://github.com/afgane/galaxy-tools-playbook>
afgane/galaxy-tools-playbook ยท
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/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.ba...@gmail.com<mailto:dannon.ba...@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
<w...@centrilliontech.com<mailto:w...@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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___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
https://lists.galaxyproject.org/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
