add T. brucei 927 genome to Galaxy main?

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add T. brucei 927 genome to Galaxy main?

swfeltz

It would be very nice to see the Trypanosoma brucei TREU927 genome added to Galaxy:

 

http://tritrypdb.org/common/downloads/Current_Release/TbruceiTREU927/fasta/data/TriTrypDB-6.0_TbruceiTREU927_Genome.fasta

 

 

Thanks

Susanne

 

 


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Re: add T. brucei 927 genome to Galaxy main?

Jen Hillman-Jackson
Hi Susanne,

I wasn't able to locate this exact assembly at NCBI - is it there? Is there a known reason why it isn't? We have a general guideline to include genomes that are published there, although there is some leeway for open source, finished (or at least not early stage draft) genomes from other sources.
I'll need to review (credits, usage, status, etc.).

Please have a look and write back with more details of what you know about this one (can be direct to me), so I don't miss anything.

Thanks!

Jen
Galaxy team

On 1/13/14 9:23 AM, Susanne Warrenfeltz wrote:

It would be very nice to see the Trypanosoma brucei TREU927 genome added to Galaxy:

 

http://tritrypdb.org/common/downloads/Current_Release/TbruceiTREU927/fasta/data/TriTrypDB-6.0_TbruceiTREU927_Genome.fasta

 

 

Thanks

Susanne

 

 



___________________________________________________________
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:

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To search Galaxy mailing lists use the unified search at:

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-- 
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:

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Jennifer Hillman-Jackson
http://galaxyproject.org
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Re: add T. brucei 927 genome to Galaxy main?

swfeltz

Hello Jen,

 

The Trypanosomas are sequenced by Sanger.  The sequences are available at GeneDB.

 

http://www.genedb.org/Homepage/Tbruceibrucei927

 

ftp://ftp.sanger.ac.uk/pub/pathogens/Trypanosoma/brucei/Latest_Whole_Genome_Sequence/Tb927_v5.2_20131108/fasta/

I work with EuPathDB (http://eupathdb.org) and some of our users are having trouble uploading larger BAM files onto our GBrowse instance. I thought it would be good to help our users convert their data into smaller file formats using Galaxy. I’m such a novice with that sort of thing, it’s been good to have your help.

 

Susanne

 

Susanne Warrenfeltz, PhD

EuPathDB Outreach

 

http://eupathdb.org

Follow us on twitter: http://twitter.com/eupathdb

FaceBook:  https://www.facebook.com/pages/EuPathDB/133123003429972

 

 

 

From: Jennifer Jackson [mailto:[hidden email]]
Sent: Monday, January 13, 2014 5:36 PM
To: Susanne Warrenfeltz; '[hidden email]'
Subject: Re: [galaxy-user] add T. brucei 927 genome to Galaxy main?

 

Hi Susanne,

I wasn't able to locate this exact assembly at NCBI - is it there? Is there a known reason why it isn't? We have a general guideline to include genomes that are published there, although there is some leeway for open source, finished (or at least not early stage draft) genomes from other sources. I'll need to review (credits, usage, status, etc.).

Please have a look and write back with more details of what you know about this one (can be direct to me), so I don't miss anything.

Thanks!

Jen
Galaxy team


On 1/13/14 9:23 AM, Susanne Warrenfeltz wrote:

It would be very nice to see the Trypanosoma brucei TREU927 genome added to Galaxy:

 

http://tritrypdb.org/common/downloads/Current_Release/TbruceiTREU927/fasta/data/TriTrypDB-6.0_TbruceiTREU927_Genome.fasta

 

 

Thanks

Susanne

 

 




___________________________________________________________
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:

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