ENA SRA data retrieval with Cloudman

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ENA SRA data retrieval with Cloudman

Mohammad Heydarian
Hi Cloudman Development Team,
I noticed on the most recent Cloudman release (revision 11219:5c789ab4144a) that there is no option to "Get Data" from the ENA SRA. We've found that retrieving large (fastq) data sets from public databases into Galaxy/Cloudman is the most convenient from the ENA SRA option in the "Get Data" menu. Will this option be coming back, or is the ENA SRA option permanently removed? 


Cheers, 
Mo Heydarian



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Re: ENA SRA data retrieval with Cloudman

Dannon Baker-2
Hey Mo,
Sorry for the super delayed response here.  I can't find a decision to remove it documented anywhere, so my guess is that this tool was unintentionally removed when we last updated the volume.  It's actually still available on disk, though, and can be re-enabled in your tool_conf.xml by adding the following back to your Get Data section:

    <tool file="data_source/ebi_sra.xml" />

-Dannon


On Mon, Mar 10, 2014 at 11:53 AM, Mohammad Heydarian <[hidden email]> wrote:
Hi Cloudman Development Team,
I noticed on the most recent Cloudman release (revision 11219:5c789ab4144a) that there is no option to "Get Data" from the ENA SRA. We've found that retrieving large (fastq) data sets from public databases into Galaxy/Cloudman is the most convenient from the ENA SRA option in the "Get Data" menu. Will this option be coming back, or is the ENA SRA option permanently removed? 


Cheers, 
Mo Heydarian



___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: ENA SRA data retrieval with Cloudman

Mohammad Heydarian
Hi Dannon,
Thanks for this information. Will the ENA SRA button be enabled on the next update of Cloudman? 

Is there a protocol (or help page) available for how to re-enable tools in the 'tool_conf.xml'? One of the great things about Galaxy Cloudman is that someone who doesn't know programming (myself and many other biologists and clinicians) can seamlessly use the platform. Unfortunately, when trivial issues arise where the solution is to insert a line or two of code in the universe of Galaxy Cloudman people like me are stymied and really don't even know where to start. I know it requires work at some level, but a tutorial on "how to find your 'tool_conf.xml'" (or "dummies guide to quick Cloudman fixes") would likely be helpful to many end users (including myself). 

Thanks again, Dannon!  

Cheers, 
Mo Heydarian

PhD candidate
The Johns Hopkins School of Medicine
Department of Biological Chemistry
725 Wolfe Street
402 Biophysics
Baltimore, MD 21205


On Wed, Apr 2, 2014 at 5:03 PM, Dannon Baker <[hidden email]> wrote:
Hey Mo,
Sorry for the super delayed response here.  I can't find a decision to remove it documented anywhere, so my guess is that this tool was unintentionally removed when we last updated the volume.  It's actually still available on disk, though, and can be re-enabled in your tool_conf.xml by adding the following back to your Get Data section:

    <tool file="data_source/ebi_sra.xml" />

-Dannon


On Mon, Mar 10, 2014 at 11:53 AM, Mohammad Heydarian <[hidden email]> wrote:
Hi Cloudman Development Team,
I noticed on the most recent Cloudman release (revision 11219:5c789ab4144a) that there is no option to "Get Data" from the ENA SRA. We've found that retrieving large (fastq) data sets from public databases into Galaxy/Cloudman is the most convenient from the ENA SRA option in the "Get Data" menu. Will this option be coming back, or is the ENA SRA option permanently removed? 


Cheers, 
Mo Heydarian



___________________________________________________________
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/



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Re: ENA SRA data retrieval with Cloudman

Dannon Baker-2
On Wed, Apr 2, 2014 at 6:03 PM, Mohammad Heydarian <[hidden email]> wrote:
Hi Dannon,
Thanks for this information. Will the ENA SRA button be enabled on the next update of Cloudman? 

I'll check to make sure there wasn't a good reason to remove it (couldn't find one in my first pass, and it's available on main, so it should be in the cloud), but yes.

Is there a protocol (or help page) available for how to re-enable tools in the 'tool_conf.xml'?

With everything headed to the toolshed, hopefully this is a thing of the past very soon.  The only documentation I found on the wiki is here: https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial

In short, you'll need to:

1) ssh to your cloud galaxy instance
2) navigate to /mnt/galaxy/galaxy-app
3) open tool_conf.xml in your favorite editor, and add the line below, exactly, in the Get Data section (the first one, begins on line 3):

 <tool file="data_source/ebi_sra.xml" />

4) Close down ssh,
5) In a web browser, go to the cloud admin panel and click restart for the Galaxy service.

 
One of the great things about Galaxy Cloudman is that someone who doesn't know programming (myself and many other biologists and clinicians) can seamlessly use the platform. Unfortunately, when trivial issues arise where the solution is to insert a line or two of code in the universe of Galaxy Cloudman people like me are stymied and really don't even know where to start.  I know it requires work at some level, but a tutorial on "how to find your 'tool_conf.xml'" (or "dummies guide to quick Cloudman fixes") would likely be helpful to many end users (including myself). 

We definitely do try to make it as ready-to-go out of the box as possible, but that's a great idea.  I'll try to document this better.
 
Thanks again, Dannon!

Anytime, thanks for your patience and for using Galaxy/Cloudman!

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Re: ENA SRA data retrieval with Cloudman

Mohammad Heydarian
Hi Dannon, 
Thanks so much, your protocol was extremely helpful!

Thanks for looking into ENA SRA. In our experience, the ENA SRA is the easiest and most reliable way of importing public NGS data into Galaxy. The ENA SRA has an actual button to click that will import your data set of choice into Galaxy, while retaining the data set ID. It is much more straight forward (and reliable) than using any of the NCBI databases. 

Thanks for your help with all of this, Dannon! Have a great night. 

Cheers, 
Mo Heydarian

PhD candidate
The Johns Hopkins School of Medicine
Department of Biological Chemistry
725 Wolfe Street
402 Biophysics
Baltimore, MD 21205


On Wed, Apr 2, 2014 at 6:21 PM, Dannon Baker <[hidden email]> wrote:
On Wed, Apr 2, 2014 at 6:03 PM, Mohammad Heydarian <[hidden email]> wrote:
Hi Dannon,
Thanks for this information. Will the ENA SRA button be enabled on the next update of Cloudman? 

I'll check to make sure there wasn't a good reason to remove it (couldn't find one in my first pass, and it's available on main, so it should be in the cloud), but yes.

Is there a protocol (or help page) available for how to re-enable tools in the 'tool_conf.xml'?

With everything headed to the toolshed, hopefully this is a thing of the past very soon.  The only documentation I found on the wiki is here: https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial

In short, you'll need to:

1) ssh to your cloud galaxy instance
2) navigate to /mnt/galaxy/galaxy-app
3) open tool_conf.xml in your favorite editor, and add the line below, exactly, in the Get Data section (the first one, begins on line 3):

 <tool file="data_source/ebi_sra.xml" />

4) Close down ssh,
5) In a web browser, go to the cloud admin panel and click restart for the Galaxy service.

 
One of the great things about Galaxy Cloudman is that someone who doesn't know programming (myself and many other biologists and clinicians) can seamlessly use the platform. Unfortunately, when trivial issues arise where the solution is to insert a line or two of code in the universe of Galaxy Cloudman people like me are stymied and really don't even know where to start.  I know it requires work at some level, but a tutorial on "how to find your 'tool_conf.xml'" (or "dummies guide to quick Cloudman fixes") would likely be helpful to many end users (including myself). 

We definitely do try to make it as ready-to-go out of the box as possible, but that's a great idea.  I'll try to document this better.
 
Thanks again, Dannon!

Anytime, thanks for your patience and for using Galaxy/Cloudman!


___________________________________________________________
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in your mail client.  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:
  http://galaxyproject.org/search/mailinglists/