On 4 March 2016 at 20:47, William Ge <w...@centrilliontech.com> wrote:
> Thanks a lot, Marius! > > Sure, you're welcome! > 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. > > > The galaxy team definitely aims for this, and usually you should (tm) be able to clone galaxy and use run.sh to get going. If you can tell us the steps where you were struggling we can try to update or clarify the documentation (A lot of it is on the wiki). > 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? > > > This is indeed a python2.6 issue. Note that python2.6 has reached it's EOL in October 2013 (https://www.python.org/download/releases/2.6.9/), and python2.6 support for galaxy will be phased out with the next release ( https://github.com/galaxyproject/galaxy/issues/1596), so it's probably a good idea to look into migrating to python2.7. That said, you can try this patch https://github.com/galaxyproject/ansible-galaxy-tools/compare/master...galaxyproject:python26_workaround.diff In addition, there may be a bioblend problem in combination with recent galaxy releases. I'll let you know once this is sorted out. 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 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 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> > 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> 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> >>> *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 >>> <https://github.com/afgane/galaxy-tools-playbook> >>> afgane/galaxy-tools-playbook ยท GitHub >>> <https://github.com/afgane/galaxy-tools-playbook> >>> 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> 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> >>>> 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 >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> ___________________________________________________________ >>>>> 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/ >>>> >>> >>> >> >
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