List of genomes

classic Classic list List threaded Threaded
2 messages Options
| Threaded
Open this post in threaded view
|

List of genomes

Lee Katz
Hi, I am wondering what I can do to add more genomes to this list (hopefully this image will make it through the mailing list).  I am importing fastq files from a MiSeq run.  We are using a modified version of Galaxy called Tron.

Everything I see on the wiki is about adding custom reference genome assemblies, but I don't understand what to do about adding a species without the reference assembly. Without the correct species, I am forced to use the option "unspecified (?)" 

Thanks for your help.

Inline image 3


--
Lee Katz, Ph.D.

___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  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/
| Threaded
Open this post in threaded view
|

Re: List of genomes

Jeremy Goecks
You can add genomes in this file:

$GALAXYROOT/tool-data/shared/ucsc/builds.txt

Note that without related files (e.g. genome sequence, indices for mapping), the build information isn't very useful. However, with an entry in this file, you can link it to other resources when they become available via .loc files:

<a href="http://wiki.galaxyproject.org/Admin/Data Integration">http://wiki.galaxyproject.org/Admin/Data%20Integration

Good luck,
J.

On May 6, 2013, at 11:53 AM, Lee Katz wrote:

Hi, I am wondering what I can do to add more genomes to this list (hopefully this image will make it through the mailing list).  I am importing fastq files from a MiSeq run.  We are using a modified version of Galaxy called Tron.

Everything I see on the wiki is about adding custom reference genome assemblies, but I don't understand what to do about adding a species without the reference assembly. Without the correct species, I am forced to use the option "unspecified (?)" 

Thanks for your help.

<image.png>


--
Lee Katz, Ph.D.
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  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/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  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/