Re: [galaxy-dev] ERROR: PIP is not a legl parament of an Ansible Play

Okay, that was a bit too short for the tool_list.yml. What is important is that you either have the tool_panel_section_label or tool_panel_section_id included in your tool_list.yml (for each tool!). Then it would help us to see what is going on if you can run the playbook with the -vvvv parameter, as well as what is going on at the same time in your galaxy logs. On 21 April 2016 at 19:30, William Ge <wge(a)centrilliontech.com&gt; wrote: > Thanks, Marius! > > > > Sure, here it is: > > I followed the online instructions to git clone the master Galaxy (Feb., > 2016) and configured it for local production use with PostgreSQL and > proftp. First tried ansible to install the tools, but did not succeed. Then > tried the online admin installation of tools one-by-one. That worked, and I > installed at least one tool for each section this way. With more help from > you and others later, I got ansible-playbook to run to install the tools. > That ran OK, but did not see the tools installed show up on the web > frontend. > > > > Beginning of the tool_list.yml is the same as the one included in the > playbook/roles, except for the api_key and galaxy_instance: > > > > api_key: ‘d22b682…’ > > galaxy_instance: 127.0.0.1:8080 > > tools: > > - name: ‘column_maker’ > > owner: … > > > > > > The command I used is: ansible-playbook tools.yaml > > The playbook was downloaded end of March, following the link given on the > Galaxy tool installation guide. > > Manual installation of the tools one-by-one from the Admin web page > works. The tools installed show up on the web page. > > > > Thanks, > > Bill > > *From:* Marius van den Beek [mailto:m.vandenbeek@gmail.com] > *Sent:* Thursday, April 21, 2016 9:45 AM > *To:* William Ge <wge(a)centrilliontech.com&gt; > *Cc:* Enis Afgan <enis.afgan(a)irb.hr&gt;; galaxy-dev(a)lists.galaxyproject.org > > *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an > Ansible Play > > > > Hi Bill, can you describe what exactly you have done? > > What would be good is if you could post the beginning of your > tool_list.yml file, > > the command that you used to run the playbook, the version of galaxy and > the last commit > > of the playbook you are using (the last entry of `git log`). > > For any of this to work you should also be able manually install tools > from the toolshed. > > Does this work for you? > > > > On 21 April 2016 at 18:14, William Ge <wge(a)centrilliontech.com&gt; wrote: > > Does anyone know why Ansible installation of the tools did not update the > shed_tools_conf.xml file to reflect the installed tools? How can I make the > tools installed with the Ansible playbook visible on the web front end? > > Thanks, > > Bill > > > > *From:* Enis Afgan [mailto:enis.afgan@irb.hr] > *Sent:* Friday, April 8, 2016 9:19 AM > > > *To:* William Ge <wge(a)centrilliontech.com&gt; > *Cc:* Marius van den Beek <m.vandenbeek(a)gmail.com&gt;; > galaxy-dev(a)lists.galaxyproject.org > *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an > Ansible Play > > > > The location of that dir is defined in shed_tool_conf.xml[.sample] and > defaults to ../shed_tools. The reasoning is described here, under item #2: > https://wiki.galaxyproject.org/DevNewsBriefs/2012_10_23#Tool_Shed > > > > On Thu, Apr 7, 2016 at 11:09 AM, William Ge <wge(a)centrilliontech.com&gt; > wrote: > > Thanks, Enis! > > Yes, that line was uncommented with the option pointing to > “tool_conf.xml,shed_tool_conf.xml”. However, I noticed that the > “shed_tool_conf.xml” has not been changed after running the > ansible-playbook to install tools. One other thing: the shed_tools > directory was one level above the Galaxy subdirectories: i.e., all > subdirectories (config, database, tool-data, tools, static, etc) are in > /home/galaxy/galaxy, while “shed_tools” is in /home/galaxy. Do not know why. > > > > Thanks, > > Bill > > > > *From:* Enis Afgan [mailto:enis.afgan@irb.hr] > *Sent:* Thursday, April 7, 2016 7:06 AM > *To:* William Ge <wge(a)centrilliontech.com&gt; > *Cc:* Marius van den Beek <m.vandenbeek(a)gmail.com&gt;; > galaxy-dev(a)lists.galaxyproject.org > > > *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an > Ansible Play > > > > Hi Bill, > > Do you have the value set in Galaxy's *$GALAXY_ROOT/config/galaxy.ini* > file for setting *tool_config_file *option? I believe this variable > should be set to a file other than the default **.sample*. > > > > On Wed, Apr 6, 2016 at 9:21 PM, William Ge <wge(a)centrilliontech.com&gt; > wrote: > > Hi, Marius, > > > > I got ansible running and installed the tools on my local instance of > Galaxy. However, the tools are not shown on the tool panel on the web page. > Wonder if the tools has been installed in the wrong place, or something > else is wrong. Have been searching the Wiki and list without any resulst. > Please point me to the right directions. > > > > Thanks, > > Bill > > > > *From:* Marius van den Beek [mailto:m.vandenbeek@gmail.com] > *Sent:* Friday, March 4, 2016 12:27 PM > *To:* William Ge <wge(a)centrilliontech.com&gt; > *Cc:* Dannon Baker <dannon.baker(a)gmail.com&gt;; > galaxy-dev(a)lists.galaxyproject.org > *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an > Ansible Play > > > > On 4 March 2016 at 20:47, William Ge <wge(a)centrilliontech.com&gt; wrote: > > Thanks a lot, Marius! > > Sure, you're welcome! > > > > I am a newbie to this complex system and want a quick clone/install > locally. I have spent over two weeks on the process. There are many > configuration files and environment variables or dependencies to sort out. > I wish the sample configuration files would include most of the options so > that new installation just needs to comment out or delete unwanted ones. > > > > The galaxy team definitely aims for this, and usually you should (tm) be > able to clone galaxy and use run.sh to get going. > > If you can tell us the steps where you were struggling we can try to > update or clarify the documentation (A lot of it is on the wiki). > > Anyway, here is the error I got: > > [galaxy@Pegasus ansible-galaxy-tools]$ 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? > > > ___________________________________________________________ > 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/ > > > > > > >