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