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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