Re: [galaxy-user] aaChanges

[Jennifer Jackson]

Hello David,

The main hub for administration tasks is:
http://galaxyproject.org/Admin

To set up data, please see "Data Integration" and "NGS Local Setup".

If this is just your own local instance, you may not need to follow all 
of the procedures. And you are correct, any log in would be specific to 
your instance.


Hopefully this helps,

Best,

Jen
Galaxy team


On 8/29/11 5:01 PM, David Joly wrote:

Thanks! I decided to install a local instance of Galaxy. The
installation went fine, but now
I'm not sure how to add a custom genome. I found some information in
past comments on the user list but I'm not sure I understand everything.
All I've got is a fasta file with all my supercontigs and a gtf file
with the predicted models.
And a somewhat basic question: am I supposed to be able to log in a
local instance? It doesn't recognize my username and password, which I
guess is normal since it is local, so what should I do?
Cheers,
David
2011/8/26 Jennifer Jackson mailto:j...@bx.psu.edu>>

===>  Please use "Reply All" when responding to this email!<===

Hello David,

You are correct, this tool will only function when a database is
defined with Galaxy already. This will include databases from UCSC
and other sources and it sounds like you have already checked using
the "Edit Attributes" form (pencil icon).

Using a custom genome currently would require a local instance where
you could add you own genomes to the list of available databases.
http://getgalaxy.org 

This may be a requirement that could be changed (ability to leave
database as unassigned). I opened a request ticket that you can
follow to see the review result for this proposal:

https://bitbucket.org/galaxy/__galaxy-central/issue/649/__modify-aachanges-tool-to-__allow-undefined



Thanks for sending in the suggestion!

Best,

Jen
Galaxy team


On 8/25/11 3:51 PM, David Joly wrote:


Hi everybody,
Maybe a dumb question but does someone know if we can use the
aaChanges
tool on a custom genome? I have my SNP dataset and my gene
dataset but I
can only assign them to one of the genome build already in
UCSC... I am
using the web server of galaxy. Do I need to install my own local
instance of Galaxy in order to add a custom genome build?
Thanks,
David


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--
Jennifer Jackson
http://usegalaxy.org 
http://galaxyproject.org/__Support 




--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
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Re: [galaxy-user] aaChanges

[David Joly]

Thanks! I decided to install a local instance of Galaxy. The installation
went fine, but now
I'm not sure how to add a custom genome. I found some information in past
comments on the user list but I'm not sure I understand everything. All I've
got is a fasta file with all my supercontigs and a gtf file with the
predicted models.

And a somewhat basic question: am I supposed to be able to log in a local
instance? It doesn't recognize my username and password, which I guess is
normal since it is local, so what should I do?

Cheers,

David




2011/8/26 Jennifer Jackson 

> ===>  Please use "Reply All" when responding to this email!<===
>
> Hello David,
>
> You are correct, this tool will only function when a database is defined
> with Galaxy already. This will include databases from UCSC and other sources
> and it sounds like you have already checked using the "Edit Attributes" form
> (pencil icon).
>
> Using a custom genome currently would require a local instance where you
> could add you own genomes to the list of available databases.
> http://getgalaxy.org
>
> This may be a requirement that could be changed (ability to leave database
> as unassigned). I opened a request ticket that you can follow to see the
> review result for this proposal:
> https://bitbucket.org/galaxy/**galaxy-central/issue/649/**
> modify-aachanges-tool-to-**allow-undefined
>
> Thanks for sending in the suggestion!
>
> Best,
>
> Jen
> Galaxy team
>
>
> On 8/25/11 3:51 PM, David Joly wrote:
>
>>
>> Hi everybody,
>> Maybe a dumb question but does someone know if we can use the aaChanges
>> tool on a custom genome? I have my SNP dataset and my gene dataset but I
>> can only assign them to one of the genome build already in UCSC... I am
>> using the web server of galaxy. Do I need to install my own local
>> instance of Galaxy in order to add a custom genome build?
>> 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/
>>
>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/**Support 
>
___
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
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Re: [galaxy-user] aaChanges

[Jennifer Jackson]

===> Please use "Reply All" when responding to this email! <===

===>  Please use "Reply All" when responding to this email!<===

Hello David,

You are correct, this tool will only function when a database is defined 
with Galaxy already. This will include databases from UCSC and other 
sources and it sounds like you have already checked using the "Edit 
Attributes" form (pencil icon).


Using a custom genome currently would require a local instance where you 
could add you own genomes to the list of available databases.

http://getgalaxy.org

This may be a requirement that could be changed (ability to leave 
database as unassigned). I opened a request ticket that you can follow 
to see the review result for this proposal:

https://bitbucket.org/galaxy/galaxy-central/issue/649/modify-aachanges-tool-to-allow-undefined

Thanks for sending in the suggestion!

Best,

Jen
Galaxy team


On 8/25/11 3:51 PM, David Joly wrote:


Hi everybody,
Maybe a dumb question but does someone know if we can use the aaChanges
tool on a custom genome? I have my SNP dataset and my gene dataset but I
can only assign them to one of the genome build already in UCSC... I am
using the web server of galaxy. Do I need to install my own local
instance of Galaxy in order to add a custom genome build?
Thanks,
David


___
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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/


--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
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Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
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Re: [galaxy-user] aaChanges / BED-to-Codon

[Jennifer Jackson]

Hello Chris,

Thank you for reporting the problem, it was indeed a calculation error 
with the BED-to-Codon operation. The code has been corrected, but has 
not been placed onto the Galaxy main server yet. Look for it in the next 
week and please let us know if you have more comments.


Thanks again!

Best,

Jen
Galaxy team

On 3/22/11 4:52 AM, Christopher Schroeder wrote:

Hello list,

I already analysed some of our data with your framework and I want to
thank you for your great work. But lately I stumbled on some strange
behavior - I used the “aaChanges”-tool, as well as the Gene
“BED-to-Codon”-tool with the same Gene-BED-File and compared the
results. What I did:

#example BED-file:

chr17  3763624 3794037 uc002fwt.2  0  -  
3765504 3788981 0  16
1953,104,129,88,74,54,200,89,22,37,134,52,54,48,403,51,
0,5577,9156,9470,12223,13078,15892,20015,21296,22197,22711,23098,23553,24049,24997,30362,

#example-output of “aaChanges”

chr17 3775847 3775848 C uc002fwt.2 Glu:Gly 375 T

#example-output of “BED-to-Codon”

chr17  3773172 3773175 uc002fwt.2  0  -

chr17  3773175 3773178 uc002fwt.2  0  -

chr17  3773178 3773181 uc002fwt.2  0  -

chr17  3775849 3775852 uc002fwt.2  0  -

chr17  3775852 3775855 uc002fwt.2  0  -

Comparing both results, the “BED-to-Codon” actually presents no codon at
position 3775848 – here the fist codon is starting at 3775849. But in
fact, looking at the ucsc browser, “aaChanges” is right. There are
another few examples (~5/1500 snps) and apparently most of them are
positions among the first codon in an exon.

Did anyone meet this problem before? What is my mistake?

Thank you.

Regards

Chris



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--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org
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Galaxy analysis and other features on the public server
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using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
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To manage your subscriptions to this and other Galaxy lists,
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