Re: [galaxy-dev] configuration management, tool shed and tool revisions

[Steve.Mcmahon]

Thanks Martin,

We can probably make use of the approach used in the Ansible-galaxy-tools role.

Regards.

Steve McMahon
Solution Architect and Senior System Administrator | Scientific Computing
Information Management and Technology
CSIRO
T +61 2 6214 2968 Alt +61 4 0077 9318
steve.mcma...@csiro.au | www.csiro.au
1 Wilf Crane Crescent, Yarralumla ACT 2600

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From: Martin Čech [mailto:mar...@bx.psu.edu]
Sent: Monday, 25 January 2016 12:38 PM
To: McMahon, Steve (IM&T, Yarralumla) ; 
galaxy-dev@lists.galaxyproject.org
Cc: Hlinka, Ondrej (IM&T, St. Lucia) ; Ludbey, Joel 
(IM&T, Clayton) 
Subject: Re: [galaxy-dev] configuration management, tool shed and tool revisions

Hello Steve,

Galaxy project's efforts in automating tool installations are mostly 
represented by the following Ansible playbook 
(https://github.com/afgane/galaxy-tools-playbook) and a role 
(https://github.com/galaxyproject/ansible-galaxy-tools).
We plan on improving that tracked at: 
https://github.com/galaxyproject/galaxy/issues/1115

The install_tool_shed_repositories.py script should install the latest revision 
when no revision is specified (and owner and repo name is present). This 
feature was added on May 14, 2014 
(https://github.com/galaxyproject/galaxy/commit/2d5c37a73f90931e03291d5c4ad6057a0e41a712).

Please let us know how it works for you.

Thank you for using Galaxy.

Martin Cech

On Sun, Jan 24, 2016 at 7:02 PM 
mailto:steve.mcma...@csiro.au>> wrote:
Hi,

We are using Puppet to manage the configuration for VMs for our development and 
production Galaxy instances.  We would like to be able to specify tool shed 
tools and their revisions and have Puppet ensure that they are installed.  Our 
Puppet code makes use of the “install_tool_shed_repositories.py” script and a 
script based on that which checks to see whether a particular tool and revision 
is installed.

We are finding that if we don’t specify the latest revision of a tool that the 
“install_tool_shed_repositories.py” script fails.  Is this what others 
experience?

I know other sites are doing configuration management with Ansible.  What 
approach are these sites taking for ensuring tools are installed or are these 
sites doing the tool installations outside of configuration management?

Regards.

Steve McMahon
Solution Architect and Senior System Administrator | Scientific Computing
Information Management and Technology
CSIRO
T +61 2 6214 2968 Alt +61 4 0077 9318
steve.mcma...@csiro.au | 
www.csiro.au
1 Wilf Crane Crescent, Yarralumla ACT 2600

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[galaxy-dev] configuration management, tool shed and tool revisions

[Steve.Mcmahon]

Hi,

We are using Puppet to manage the configuration for VMs for our development and 
production Galaxy instances.  We would like to be able to specify tool shed 
tools and their revisions and have Puppet ensure that they are installed.  Our 
Puppet code makes use of the "install_tool_shed_repositories.py" script and a 
script based on that which checks to see whether a particular tool and revision 
is installed.

We are finding that if we don't specify the latest revision of a tool that the 
"install_tool_shed_repositories.py" script fails.  Is this what others 
experience?

I know other sites are doing configuration management with Ansible.  What 
approach are these sites taking for ensuring tools are installed or are these 
sites doing the tool installations outside of configuration management?

Regards.

Steve McMahon
Solution Architect and Senior System Administrator | Scientific Computing
Information Management and Technology
CSIRO
T +61 2 6214 2968 Alt +61 4 0077 9318
steve.mcma...@csiro.au | www.csiro.au
1 Wilf Crane Crescent, Yarralumla ACT 2600

PLEASE NOTE
The information contained in this email may be confidential or privileged. Any 
unauthorised use or disclosure is prohibited. If you have received this email 
in error, please delete it immediately and notify the sender by return email. 
Thank you. To the extent permitted by law, CSIRO does not represent, warrant 
and/or guarantee that the integrity of this communication has been maintained 
or that the communication is free of errors, virus, interception or 
interference.
Please consider the environment before printing this email.

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[galaxy-dev] issue with install_tool_shed_repositories.py

[Steve.Mcmahon]

Hi,

We are doing a puppet configuration for our Galaxy service and this includes 
installing tools with the "install_tool_shed_repositories.py" script.  It seems 
that when we specify a revision for a tool which is not the latest we get an 
error

e.g.

/usr/bin/python 
/OSM/galaxy/tools/galaxy-dev-03/galaxy-dist/scripts/api/install_tool_shed_repositories.py
 --api x -l http://localhost --url http://toolshed.g2.bx.psu.edu/ 
-o devteam --name fasta_nucleotide_changer --tool-deps --repository-deps -r 
2f868bfbe9de --panel-section-id NGS_QC
HTTP Error 500: Internal Server Error
{"err_msg": "Uncaught exception in exposed API method:", "err_code": 0}

Has anyone seen this?  Shall I create an issue in Trello for it?

Our work around is to use the latest revision.  We'd probably like to not have 
to do that, however.

Cheers.
Steve McMahon
Solution Architect and Senior System Administrator | Scientific Computing
Information Management and Technology
CSIRO
T +61 2 6214 2968 Alt +61 4 0077 9318
steve.mcma...@csiro.au | www.csiro.au
1 Wilf Crane Crescent, Yarralumla ACT 2600

PLEASE NOTE
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unauthorised use or disclosure is prohibited. If you have received this email 
in error, please delete it immediately and notify the sender by return email. 
Thank you. To the extent permitted by law, CSIRO does not represent, warrant 
and/or guarantee that the integrity of this communication has been maintained 
or that the communication is free of errors, virus, interception or 
interference.
Please consider the environment before printing this email.

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