Re: [galaxy-user] add T. brucei 927 genome to Galaxy main?

2014-01-14 Thread Susanne Warrenfeltz 
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:j...@bx.psu.edu]
Sent: Monday, January 13, 2014 5:36 PM
To: Susanne Warrenfeltz; 'galaxy-user@lists.bx.psu.edu'
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:

  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-user] add T. brucei 927 genome to Galaxy main?

2014-01-13 Thread Jennifer 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:

   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/