________________________________ From: Marius van den Beek <m.vandenb...@gmail.com> Sent: Friday, March 4, 2016 12:26 PM 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 Thanks, Marius! That got me through! The Galaxy Team has done a wonderful job putting together such a complex system. It is very well packaged and documented good enough for developers. But for new people like me, a more fool-proof step-by-step guide will be very helpful. I have worked with ACEDB, GCG, LionBioscience SRS and other early bioinformatics packages in the past, but have been out of touch for a while. The most challenging portion for me is to sort out the configuration files, retrieve/download data and install tools. The web admin application is a good tool. It would be very helpful for new people if there is a check box in front of the categories of tools, and in front of each individual tools, so that we can check to select and click install to perform batch install there. Best regards, Bill On 4 March 2016 at 20:47, William Ge <w...@centrilliontech.com<mailto: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<mailto:m.vandenb...@gmail.com>> Sent: Friday, March 4, 2016 11:03 AM To: William Ge Cc: Dannon Baker; 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 The list of tools installed on usegalaxy.org<http://usegalaxy.org/> is conviniently desposited here: Galaxy<http://usegalaxy.org/> usegalaxy.org<http://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 ___________________________________________________________ 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/
___________________________________________________________ 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/
