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