[galaxy-user] Experience with Loading NGS data on standalone instance of galaxy

[Abhishek Pratap]

Hi Nate
Explicitly specifying the files names make the upload to work the way I
expected it should. I am planning to discuss few of such changes with
Anton/Greg sometime next month specially in context of NGS related data.

Also when the data is exported from library to history for analysis, is is
actually copied ? I see that part taking considerable time.

Thanks,
-Abhi

On Thu, Oct 8, 2009 at 3:37 PM, Nate Coraor <nate at bx.psu.edu> wrote:

> Abhishek Pratap wrote:
>
>  Based on the testing of the new feature I am not sure if it working as
>> expected. I gave galaxy a path to GERALD folder (which is a analysis folder
>> generated by Illumina pipeline) and selected file type to be just
>> "solexafastq". It took about two hours for the process to be completed.
>> Somehow it went through each file and uploaded everything in the library.
>> Ideally it should look up only the relevant fastq files and upload total of
>> 8 files (1 / lane ) present in the folder. This process should be very fast
>> as it would just record the path.
>>
>
> Hi Abhi,
>
> The file type selector doesn't determine what type of files to search for -
> partially because it predates any sort of multiple upload feature, and
> partially because it's not always possible to trust a file's extension (if
> it even has a recognizable extension).  If such a feature would be useful, a
> feature request can certainly be created for it.
>
> If you only need 8 files out of a large directory of files, it'd be best to
> simply paste the path to those 8 files in the upload box.
>
> Also, be sure you're checking "No" to the "Copy data into Galaxy?" box to
> ensure data is only "linked" and not copied.
>
> --nate
>
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