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 <w...@centrilliontech.com> 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.af...@irb.hr] > *Sent:* Friday, April 8, 2016 9:19 AM > > *To:* William Ge <w...@centrilliontech.com> > *Cc:* Marius van den Beek <m.vandenb...@gmail.com>; > galaxy-dev@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 <w...@centrilliontech.com> > 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.af...@irb.hr] > *Sent:* Thursday, April 7, 2016 7:06 AM > *To:* William Ge <w...@centrilliontech.com> > *Cc:* Marius van den Beek <m.vandenb...@gmail.com>; > galaxy-dev@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 *$GALAXY_ROOT/config/galaxy.ini* > file for setting *tool_config_file *option? I believe this variable > should be set to a file other than the default **.sample*. > > > > On Wed, Apr 6, 2016 at 9:21 PM, William Ge <w...@centrilliontech.com> > wrote: > > Hi, Marius, > > > > I got ansible running and installed the tools on my local instance of > Galaxy. However, the tools are not shown on the tool panel on the web page. > Wonder if the tools has been installed in the wrong place, or something > else is wrong. Have been searching the Wiki and list without any resulst. > Please point me to the right directions. > > > > Thanks, > > Bill > > > > *From:* Marius van den Beek [mailto:m.vandenb...@gmail.com] > *Sent:* Friday, March 4, 2016 12:27 PM > *To:* William Ge <w...@centrilliontech.com> > *Cc:* Dannon Baker <dannon.ba...@gmail.com>; > galaxy-dev@lists.galaxyproject.org > *Subject:* Re: [galaxy-dev] ERROR: PIP is not a legl parament of an > Ansible Play > > > > On 4 March 2016 at 20:47, William Ge <w...@centrilliontech.com> wrote: > > Thanks a lot, Marius! > > Sure, you're welcome! > > > > I am a newbie to this complex system and want a quick clone/install > locally. I have spent over two weeks on the process. There are many > configuration files and environment variables or dependencies to sort out. > I wish the sample configuration files would include most of the options so > that new installation just needs to comment out or delete unwanted ones. > > > > The galaxy team definitely aims for this, and usually you should (tm) be > able to clone galaxy and use run.sh to get going. > > If you can tell us the steps where you were struggling we can try to > update or clarify the documentation (A lot of it is on the wiki). > > Anyway, here is the error I got: > > [galaxy@Pegasus ansible-galaxy-tools]$ 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? > > > ___________________________________________________________ > 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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