add nglims to galaxy-dist

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add nglims to galaxy-dist

Peter Huang

Hi Brad,

 

I am curious if you could tell me the way that I could add your nglims to my galaxy-dist production system. I have read your step by step procedure here: http://wiki.galaxyproject.org/Admin/Sample%20Tracking/Next%20Gen

 

but it didn’t mention how to add it to the galaxy-dist. Do you have a patch name for it? Should I use hg pull or hg patch? Thanks

 

Best,

 

Peter


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Re: add nglims to galaxy-dist

Brad Chapman

Peter;
I maintain nglims as a fork of galaxy-central, syncing back to the main
repository regularly:

https://bitbucket.org/chapmanb/galaxy-central

This was an easier approach than trying to keep a set of patches up to
date. Hope this helps,
Brad


> Hi Brad,
>
> I am curious if you could tell me the way that I could add your nglims to my galaxy-dist production system. I have read your step by step procedure here: http://wiki.galaxyproject.org/Admin/Sample%20Tracking/Next%20Gen
>
> but it didn't mention how to add it to the galaxy-dist. Do you have a patch name for it? Should I use hg pull or hg patch? Thanks
>
> Best,
>
> Peter
> ___________________________________________________________
> 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/
___________________________________________________________
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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Re: add nglims to galaxy-dist

Peter Huang
Hi Brad,

Thanks for the kind reply. So does it mean that I won't be able to add it to our existing galaxy-dist production server as the only way to obtain it is to clone the one you listed? Thanks.

Best,

Peter

-----Original Message-----
From: Brad Chapman [mailto:[hidden email]]
Sent: September-17-13 9:47 PM
To: Peter Huang; [hidden email]
Subject: Re: [galaxy-user] add nglims to galaxy-dist


Peter;
I maintain nglims as a fork of galaxy-central, syncing back to the main repository regularly:

https://bitbucket.org/chapmanb/galaxy-central

This was an easier approach than trying to keep a set of patches up to date. Hope this helps, Brad


> Hi Brad,
>
> I am curious if you could tell me the way that I could add your nglims
> to my galaxy-dist production system. I have read your step by step
> procedure here:
> http://wiki.galaxyproject.org/Admin/Sample%20Tracking/Next%20Gen
>
> but it didn't mention how to add it to the galaxy-dist. Do you have a
> patch name for it? Should I use hg pull or hg patch? Thanks
>
> Best,
>
> Peter
> ___________________________________________________________
> 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/

___________________________________________________________
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/
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Re: add nglims to galaxy-dist

Brad Chapman

Peter;

> Thanks for the kind reply. So does it mean that I won't be able to add
> it to our existing galaxy-dist production server as the only way to
> obtain it is to clone the one you listed? Thanks.

Unfortunately it's not that easy to graft into place on top of the
existing Galaxy. It requires a database table addition and other tweaks
so it would be a bit tricky to automate.

Additionally, my suggestion would be to first try it out on a separate
instance before thinking about integrating with your production Galaxy.
It does take a bit of tweaking and it would be good to see if it fit
your needs before investing time in it.

Sorry the process isn't easier and hope this helps,
Brad


> -----Original Message-----
> From: Brad Chapman [mailto:[hidden email]]
> Sent: September-17-13 9:47 PM
> To: Peter Huang; [hidden email]
> Subject: Re: [galaxy-user] add nglims to galaxy-dist
>
>
> Peter;
> I maintain nglims as a fork of galaxy-central, syncing back to the main repository regularly:
>
> https://bitbucket.org/chapmanb/galaxy-central
>
> This was an easier approach than trying to keep a set of patches up to date. Hope this helps, Brad
>
>
>> Hi Brad,
>>
>> I am curious if you could tell me the way that I could add your nglims
>> to my galaxy-dist production system. I have read your step by step
>> procedure here:
>> http://wiki.galaxyproject.org/Admin/Sample%20Tracking/Next%20Gen
>>
>> but it didn't mention how to add it to the galaxy-dist. Do you have a
>> patch name for it? Should I use hg pull or hg patch? Thanks
>>
>> Best,
>>
>> Peter
>> ___________________________________________________________
>> 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/
___________________________________________________________
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/
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Re: add nglims to galaxy-dist

Peter Huang
Hi Brad,

Thanks for the email reply. As you suggested, I installed a second instance of galaxy (ie galaxy-central from your branch). I was able to follow all what you wrote. However, when I tried to launch the galaxy, the 'next gen sequence' menu wasn't there under the Lab tab. I watch the video you posted at the youtube, but still couldn't find it. Do you know what I miss here? Thanks.

Best,

Peter

-----Original Message-----
From: Brad Chapman [mailto:[hidden email]]
Sent: September-18-13 8:44 PM
To: Peter Huang; [hidden email]
Subject: RE: [galaxy-user] add nglims to galaxy-dist


Peter;

> Thanks for the kind reply. So does it mean that I won't be able to add
> it to our existing galaxy-dist production server as the only way to
> obtain it is to clone the one you listed? Thanks.

Unfortunately it's not that easy to graft into place on top of the existing Galaxy. It requires a database table addition and other tweaks so it would be a bit tricky to automate.

Additionally, my suggestion would be to first try it out on a separate instance before thinking about integrating with your production Galaxy.
It does take a bit of tweaking and it would be good to see if it fit your needs before investing time in it.

Sorry the process isn't easier and hope this helps, Brad


> -----Original Message-----
> From: Brad Chapman [mailto:[hidden email]]
> Sent: September-17-13 9:47 PM
> To: Peter Huang; [hidden email]
> Subject: Re: [galaxy-user] add nglims to galaxy-dist
>
>
> Peter;
> I maintain nglims as a fork of galaxy-central, syncing back to the main repository regularly:
>
> https://bitbucket.org/chapmanb/galaxy-central
>
> This was an easier approach than trying to keep a set of patches up to
> date. Hope this helps, Brad
>
>
>> Hi Brad,
>>
>> I am curious if you could tell me the way that I could add your
>> nglims to my galaxy-dist production system. I have read your step by
>> step procedure here:
>> http://wiki.galaxyproject.org/Admin/Sample%20Tracking/Next%20Gen
>>
>> but it didn't mention how to add it to the galaxy-dist. Do you have a
>> patch name for it? Should I use hg pull or hg patch? Thanks
>>
>> Best,
>>
>> Peter
>> ___________________________________________________________
>> 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/

___________________________________________________________
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/
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Re: add nglims to galaxy-dist

Brad Chapman

Peter;
Thanks for giving this a try. The set of instructions to get this up and
running are here:

http://wiki.galaxyproject.org/Admin/Sample%20Tracking/Next%20Gen

If the `Next Gen sequence` menu is missing, the most likely cause is
that you don't have `use_nglims=True` set in your `universe_wsgi.ini`
file.

Hope this helps get it running,
Brad


> Hi Brad,
>
> Thanks for the email reply. As you suggested, I installed a second instance of galaxy (ie galaxy-central from your branch). I was able to follow all what you wrote. However, when I tried to launch the galaxy, the 'next gen sequence' menu wasn't there under the Lab tab. I watch the video you posted at the youtube, but still couldn't find it. Do you know what I miss here? Thanks.
>
> Best,
>
> Peter
>
> -----Original Message-----
> From: Brad Chapman [mailto:[hidden email]]
> Sent: September-18-13 8:44 PM
> To: Peter Huang; [hidden email]
> Subject: RE: [galaxy-user] add nglims to galaxy-dist
>
>
> Peter;
>
>> Thanks for the kind reply. So does it mean that I won't be able to add
>> it to our existing galaxy-dist production server as the only way to
>> obtain it is to clone the one you listed? Thanks.
>
> Unfortunately it's not that easy to graft into place on top of the existing Galaxy. It requires a database table addition and other tweaks so it would be a bit tricky to automate.
>
> Additionally, my suggestion would be to first try it out on a separate instance before thinking about integrating with your production Galaxy.
> It does take a bit of tweaking and it would be good to see if it fit your needs before investing time in it.
>
> Sorry the process isn't easier and hope this helps, Brad
>
>
>> -----Original Message-----
>> From: Brad Chapman [mailto:[hidden email]]
>> Sent: September-17-13 9:47 PM
>> To: Peter Huang; [hidden email]
>> Subject: Re: [galaxy-user] add nglims to galaxy-dist
>>
>>
>> Peter;
>> I maintain nglims as a fork of galaxy-central, syncing back to the main repository regularly:
>>
>> https://bitbucket.org/chapmanb/galaxy-central
>>
>> This was an easier approach than trying to keep a set of patches up to
>> date. Hope this helps, Brad
>>
>>
>>> Hi Brad,
>>>
>>> I am curious if you could tell me the way that I could add your
>>> nglims to my galaxy-dist production system. I have read your step by
>>> step procedure here:
>>> http://wiki.galaxyproject.org/Admin/Sample%20Tracking/Next%20Gen
>>>
>>> but it didn't mention how to add it to the galaxy-dist. Do you have a
>>> patch name for it? Should I use hg pull or hg patch? Thanks
>>>
>>> Best,
>>>
>>> Peter
>>> ___________________________________________________________
>>> 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/
___________________________________________________________
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/