uploading large datasets into a new instance of Galaxy on a Mac Pro

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uploading large datasets into a new instance of Galaxy on a Mac Pro

Elwood Linney

Hello,
I installed Galaxy on a new Mac Pro with 64gb of ram and a solid state first drive and 3 , 2tb normal drives.

I can upload from my desktop a smaller file like a reference list or a cuffdiff file but when I try to load a 16gb fastq file it just does not load.

Given that I have my files on the same computer that has Galaxy, and given that I am not well versed in unix, would anyone have a suggestion as to ways I could easily upload these large files.

I would like to think I am just naive and that this has a simple solution.  Hopefully this is the correct list to pose this question.

Thank you for any help,

el linney

For those in the no, I did see this appear on the terminal after I tried to upload the file through the browser mechanism for upload:

"Overflow Error:  signed integer is greater than maximum"

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Re: uploading large datasets into a new instance of Galaxy on a Mac Pro

Adam Brenner
How are you trying to upload the data to Galaxy? Are you using the web
interface? Or...?

--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences

Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/

University of California, Irvine
www.ics.uci.edu/~aebrenne/
[hidden email]

On Fri, May 31, 2013 at 1:59 PM, Elwood Linney <[hidden email]> wrote:

>
> Hello,
> I installed Galaxy on a new Mac Pro with 64gb of ram and a solid state first
> drive and 3 , 2tb normal drives.
>
> I can upload from my desktop a smaller file like a reference list or a
> cuffdiff file but when I try to load a 16gb fastq file it just does not
> load.
>
> Given that I have my files on the same computer that has Galaxy, and given
> that I am not well versed in unix, would anyone have a suggestion as to ways
> I could easily upload these large files.
>
> I would like to think I am just naive and that this has a simple solution.
> Hopefully this is the correct list to pose this question.
>
> Thank you for any help,
>
> el linney
>
> For those in the no, I did see this appear on the terminal after I tried to
> upload the file through the browser mechanism for upload:
>
> "Overflow Error:  signed integer is greater than maximum"
>
> ___________________________________________________________
> 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: uploading large datasets into a new instance of Galaxy on a Mac Pro

Dannon Baker-2
In reply to this post by Elwood Linney
Upload via browser is likely to fail when file size is > 2G, but since the filesystem is local, you have a few extra options.  You'll need to be logged in as an admin to use the functionality, but if you enable allow_library_path_paste (in universe_wsgi.ini), you can create datasets in a data library (you'll need to make one) by simply pasting the full (local) file paths into the usual input box.

-Dannon


On Fri, May 31, 2013 at 4:59 PM, Elwood Linney <[hidden email]> wrote:

Hello,
I installed Galaxy on a new Mac Pro with 64gb of ram and a solid state first drive and 3 , 2tb normal drives.

I can upload from my desktop a smaller file like a reference list or a cuffdiff file but when I try to load a 16gb fastq file it just does not load.

Given that I have my files on the same computer that has Galaxy, and given that I am not well versed in unix, would anyone have a suggestion as to ways I could easily upload these large files.

I would like to think I am just naive and that this has a simple solution.  Hopefully this is the correct list to pose this question.

Thank you for any help,

el linney

For those in the no, I did see this appear on the terminal after I tried to upload the file through the browser mechanism for upload:

"Overflow Error:  signed integer is greater than maximum"

___________________________________________________________
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/


___________________________________________________________
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/