Adding custom genome builds to a galaxy instance

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Adding custom genome builds to a galaxy instance

dcnorris
Hi Galaxy Users,
I am trying to understand the process of adding new entries to the genome builds dropdown list and also ensuring these new genome entries are appropriately mapped to a reference sequence.  I have been working through the code to work it out myself, but it would be helpful to get some advice from another user or possibly a developer who has experience with this process to avoid possible pitfalls.  It would be a nice future enhancement to expose this functionality to administrators.  Any advice would be appreciated!
Thanks,
-David
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Re: Adding custom genome builds to a galaxy instance

Jen Hillman-Jackson
Hi David,

I think that you are asking about the locally cached reference genome
builds - also sometimes called 'built-in'? If so, these wikis have
instructions to help you create, organize, and obtain these data (if you
want copies of what we host on Main).

Reference genome builds can seem to have several "names" given to them -
but if you look closely, you will note that each contains the most
important identifier, the "dbkey". This short tag "dbkey" is what is
seen as assigned for the "database" metadata attribute in the UI. Making
sure that this is consistent and that location (e.g. ".loc" files)
contain the correct key and are in the correct format will move you in
the right direction. Watch for: tabs for white space between fields, no
extra white space, no extra lines, dbkey value used are the same as in
the reference and index files names, etc. - as described in headers of
.loc files, the wikis below, or even follow what we have in ours from
the rsync server.

https://wiki.galaxyproject.org/Admin/DataIntegration
   - The most important parts of this wiki to note are the "builds.txt"
file (this is the list of genomes in the pull down menu) and then the
rsync server instructions (this is where you can obtain copies of the
data used on Main)

https://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
   - Organizing data and building indexes for various tools.

Adding "Custom Reference Genomes" through the UI - as done by individual
users - is a different process, but I don't think you are asking about
that. The internals for that are not in a wiki, but the processing is
automatic and much is done on the fly as tools execute, when a fasta
file from the history is selected as the target reference build. (Same
indexes, just not saved beyond the genome being loaded as when added
using: User -> Custom Builds, good for using Trackster).

Hopefully this will help you get started.

Jen
Galaxy team



On 3/3/14 8:13 AM, Norris, David wrote:

> Hi Galaxy Users,
> I am trying to understand the process of adding new entries to the genome builds dropdown list and also ensuring these new genome entries are appropriately mapped to a reference sequence.  I have been working through the code to work it out myself, but it would be helpful to get some advice from another user or possibly a developer who has experience with this process to avoid possible pitfalls.  It would be a nice future enhancement to expose this functionality to administrators.  Any advice would be appreciated!
> Thanks,
> -David
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>    http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>    http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
>
>    http://galaxyproject.org/search/mailinglists/

--
Jennifer Hillman-Jackson
http://galaxyproject.org

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:

  http://galaxyproject.org/search/mailinglists/
Jennifer Hillman-Jackson
http://galaxyproject.org