Hi Srinivas,

what is the Aim of that project, do you plan to also clone the data, or only the Galaxy installation. What should be keeped, all configs, also the configs special to your hardware?


I can't really tell you where full paths are stored. grepping and a database check will probably tell you.

Cheers,
Bjoern

Am 09.07.2014 00:56, schrieb Srinivas .:
Hi Bjoern,
Thank you for the response. Thanks also for your work on Docker'izing Galaxy. 
Using the Tool Shed to create Dockerfiles also appears to have good potential 
-- thanks for exploring that possibility, Greg.
The crux of my question is on whether it is possible to clone a customized 
Galaxy installation (whether using Docker containers or VM).
As an example, the "shed_tool_data_table_conf.xml" file contains absolute paths to the 
".loc" files containing reference genomes.  Those absolute paths (unless OK to convert them to 
relative paths or a different set of absolute paths) would prevent a clone of the reference installation from 
working properly since each cloned instance would require a unique "galaxy-dist" and supporting set 
of directories (within a common cluster). To illustrate:
1. "galaxy-dist" on the master instance is located within "/export/galaxy/master/". Installing BWA 
using the Tool Shed results in a "shed_tool_data_table_conf.xml" file that contains 
"/export/galaxy/master/galaxy-dist/tool-data/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/b4427dbb6ced/bwa_index.loc"
2. "galaxy-dist" on a clone of the master instance is located within "/export/galaxy/clone-1/".  In order for 
this to work, "shed_tool_data_table_conf.xml" would have to reference the ".loc" files either using relative 
paths or updated absolute paths to reflect the proper location of the ".loc" files.  Can this be done without causing 
unknown / TBD side effect ?
I am looking for input on whether there might be other similar (surmountable / 
unsurmountable) considerations, including path dependencies within the 
database, that would make cloning a reference installation unviable.
Thanks.
Date: Mon, 7 Jul 2014 23:21:56 +0200
From: bjoern.gruen...@gmail.com
To: galaxy-dev@lists.bx.psu.edu; srinivas.gal...@outlook.com
Subject: Re: [galaxy-dev] Clonable Galaxy installation

Hi Srinivas,

I'm not sure I entirely understood your questions, its to late for me
today sorry. But maybe you would like to have a look at:

https://github.com/bgruening/docker-recipes

It's basically a docker base image (galaxy) on top you can create
several specialised images can be created (e.g. galaxy-deeptools). Every
child images is 'just' a set of toolshed tools.

Also have a look at https://trello.com/c/tm1fPvyq and try the new Test
ToolShed feature, which will create Dockerfiles for you!

Let us know how that works for you. It's still all work in progress and
can change or entirely disappear :)
Feedbacks, Pull-Requests welcome!

Cheers,
Bjoern

Am 07.07.2014 23:08, schrieb Srinivas .:
Hello,
I am writing to inquire if there are considerations which would prevent 
creation of multiple instances of Galaxy by cloning a reference Galaxy 
installation containing a pre-configured set of tools and related assets.  Both 
the reference and cloned instances would reside in the same cluster, and are 
each built within dedicated virtual machines . A Docker based approach has yet 
to be attempted but the same question likely applies.
One issue that was observed in attempting this was that the Tool Shed populates 
the “shed_tool_data_table_conf.xml” file with absolute paths to the “.loc” 
files for tools installed via the Tool Shed (even though all path related 
variables are specified using relative paths in the respective configuration 
files).  Might there be other similar dependencies or constraints, including 
those in the database, that would disallow this clonable Galaxy installation 
model from being viable ?
With regard to the Tool Shed updating files with absolute paths: Could the Toolshed be 
configured to use relative paths ? Else, would it be OK to update the "file 
path" variables within the instances created from the reference installation to 
reflect the instance-specific file paths ?
Thanks in advance.
--Srinivas
                                        



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