blast_ui add gff to output files list

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blast_ui add gff to output files list

Sofia Robb-4
Hello Lacey,

If you are interested, I made some modifications to add a gff to the output file list. i need it to load up into apollo. I am happy to share my code. I am sure you could get it done in a much more elegant way :)

Thanks for all your work with this module,
Sofia





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Re: blast_ui add gff to output files list

Cannon, Ethalinda K [COM S]

Hi Lacey and Sofia,


I have a programmer working the BLAST UI module. He has exposed its functionality via REST web services, a feature than is disabled by default. Progress is slow but we are now doing final(?) testing before submitting a pull request for the new code.


He is also planning to add a GFF download option, so it might be best, if Lacey hasn't already responded to you, to send your patch to me so that he can include it with his other changes, then to the pull request.


Lacey, does this sound okay?

Ethy


From: Sofia Robb <[hidden email]>
Sent: Tuesday, September 13, 2016 2:03 PM
To: [hidden email]; Lacey Sanderson
Subject: [Gmod-tripal] blast_ui add gff to output files list
 
Hello Lacey,

If you are interested, I made some modifications to add a gff to the output file list. i need it to load up into apollo. I am happy to share my code. I am sure you could get it done in a much more elegant way :)

Thanks for all your work with this module,
Sofia





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Re: blast_ui add gff to output files list

Kucheran, Lacey Sanderson
Hi Ethy & Sofia,

First off -Thanks Sofia! That sounds like really useful functionality :-)

I would be tempted to get Sofia to submit a pull request separately to make it easier to keep track of attribution and to keep the size of the pull requests down. Ethy --Since your group is also invested in this functionality, would you have time to look at her pull request to ensure it meets your needs as well?

~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On September 14, 2016 at 3:11:57 PM, Cannon, Ethalinda K [COM S] ([hidden email]) wrote:

Hi Lacey and Sofia,


I have a programmer working the BLAST UI module. He has exposed its functionality via REST web services, a feature than is disabled by default. Progress is slow but we are now doing final(?) testing before submitting a pull request for the new code.


He is also planning to add a GFF download option, so it might be best, if Lacey hasn't already responded to you, to send your patch to me so that he can include it with his other changes, then to the pull request.


Lacey, does this sound okay?

Ethy


From: Sofia Robb <[hidden email]>
Sent: Tuesday, September 13, 2016 2:03 PM
To: [hidden email]; Lacey Sanderson
Subject: [Gmod-tripal] blast_ui add gff to output files list
 
Hello Lacey,

If you are interested, I made some modifications to add a gff to the output file list. i need it to load up into apollo. I am happy to share my code. I am sure you could get it done in a much more elegant way :)

Thanks for all your work with this module,
Sofia





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Re: blast_ui add gff to output files list

Stephen Ficklin-2

I would agree that a  pull request is the way to go as it has many advantages and gives you, Sofia, credit for your submission!

Sofia, are you familiar with the process of performing a pull request on GitHub?

Stephen


On 9/14/2016 3:07 PM, Kucheran, Lacey Sanderson wrote:
Hi Ethy & Sofia,

First off -Thanks Sofia! That sounds like really useful functionality :-)

I would be tempted to get Sofia to submit a pull request separately to make it easier to keep track of attribution and to keep the size of the pull requests down. Ethy --Since your group is also invested in this functionality, would you have time to look at her pull request to ensure it meets your needs as well?

~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a moz-do-not-send="true" href="tel://966-3208">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On September 14, 2016 at 3:11:57 PM, Cannon, Ethalinda K [COM S] ([hidden email]) wrote:

Hi Lacey and Sofia,


I have a programmer working the BLAST UI module. He has exposed its functionality via REST web services, a feature than is disabled by default. Progress is slow but we are now doing final(?) testing before submitting a pull request for the new code.


He is also planning to add a GFF download option, so it might be best, if Lacey hasn't already responded to you, to send your patch to me so that he can include it with his other changes, then to the pull request.


Lacey, does this sound okay?

Ethy


From: Sofia Robb [hidden email]
Sent: Tuesday, September 13, 2016 2:03 PM
To: [hidden email]; Lacey Sanderson
Subject: [Gmod-tripal] blast_ui add gff to output files list
 
Hello Lacey,

If you are interested, I made some modifications to add a gff to the output file list. i need it to load up into apollo. I am happy to share my code. I am sure you could get it done in a much more elegant way :)

Thanks for all your work with this module,
Sofia






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Re: blast_ui add gff to output files list

Sofia Robb
Yes, I have done a pull request. I will likely have to revisit the documentation to make sure I do it right :)

I guess if I am going to officially share, I should rewrite my Perl gff generator into a php function :/ I can do it! 

It will be fun to contribute :)


On Wed, Sep 14, 2016 at 6:49 PM, Sofia Robb <[hidden email]> wrote:
Yes, I have done a pull request. I will likely have to revisit the documentation to make sure I do it right :)

I guess if I am going to officially share, I should rewrite my Perl gff generator into a php function :/ I can do it! 

It will be fun to contribute :)

Sofia



Sent from my iPhone

On Sep 14, 2016, at 5:51 PM, Stephen Ficklin <[hidden email]> wrote:

I would agree that a  pull request is the way to go as it has many advantages and gives you, Sofia, credit for your submission!

Sofia, are you familiar with the process of performing a pull request on GitHub?

Stephen


On 9/14/2016 3:07 PM, Kucheran, Lacey Sanderson wrote:
Hi Ethy & Sofia,

First off -Thanks Sofia! That sounds like really useful functionality :-)

I would be tempted to get Sofia to submit a pull request separately to make it easier to keep track of attribution and to keep the size of the pull requests down. Ethy --Since your group is also invested in this functionality, would you have time to look at her pull request to ensure it meets your needs as well?

~Lacey

------------------------------------------------------
Lacey-Anne Sanderson
Bioinformaticist
Pulse Crop Breeding and Genetics
Phone: (306) <a href="tel://966-3208" target="_blank">966-3208
Room 2C33 Agriculture
Department of Plant Sciences
University of Saskatchewan

On September 14, 2016 at 3:11:57 PM, Cannon, Ethalinda K [COM S] ([hidden email]) wrote:

Hi Lacey and Sofia,


I have a programmer working the BLAST UI module. He has exposed its functionality via REST web services, a feature than is disabled by default. Progress is slow but we are now doing final(?) testing before submitting a pull request for the new code.


He is also planning to add a GFF download option, so it might be best, if Lacey hasn't already responded to you, to send your patch to me so that he can include it with his other changes, then to the pull request.


Lacey, does this sound okay?

Ethy


From: Sofia Robb [hidden email]
Sent: Tuesday, September 13, 2016 2:03 PM
To: [hidden email]; Lacey Sanderson
Subject: [Gmod-tripal] blast_ui add gff to output files list
 
Hello Lacey,

If you are interested, I made some modifications to add a gff to the output file list. i need it to load up into apollo. I am happy to share my code. I am sure you could get it done in a much more elegant way :)

Thanks for all your work with this module,
Sofia






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