Re: [galaxy-dev] Loading or Upload Large datasets into Galaxy History

2016-01-28 Thread Martin Čech 
Amos,

I have no experience with the tool you mentioned and I am not surprised it
does not work correctly as it has been updated 4years ago and Galaxy has
changed in the meantime.

If you want to get your local data to your local Galaxy the best option is
to import it into Data Library and use 'link to files' option which will
prevent creating duplicates of the dataset.

Some details are available here:
https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles

I hope this helps.

thanks

Martin

On Thu, Jan 28, 2016 at 3:14 PM Raphenya, Amogelang 
wrote:

> Hi Martin,
>
> I have local instance.
>
> I uploaded 1GB fastq compressed with *.gz* using *Upload_local_file *tool
> (installed from galaxy tool shed).
>
> After the upload when I run *fastqc* it failed BUT when I upload the same
> file using *Upload_file, **fastqc *works fine.
>
> Cheers.
>
>
> *Amos Raphenya *
> *Bioinformatics Software Developer*
> *Department of Biochemistry & Biomedical Sciences*
> *McMaster University, MDCL **2317*
> *p: (905) 525-9140 **ext: **22787*
> *a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1*
> *e:  raphe...@mcmaster.ca  *
> *skype: amos_raphenya*
>
> On Jan 28, 2016, at 3:08 PM, Martin Čech  wrote:
>
> Hi Amos,
>
> what Galaxy are you using and where are you seeing these messages?
>
> thanks
>
> Martin
>
> On Thu, Jan 28, 2016 at 2:56 PM Raphenya, Amogelang 
> wrote:
>
>> Hi All,
>>
>> Is there a faster way to upload or load large datasets into galaxy
>> history without using FTP?
>>
>> I tried *Upload_local_file* (*to current history*) and it doesn’t upload
>> *.gz* files correctly as compared to when using* Upload_file *(*from
>> your computer*).
>>
>> Cheers.
>>
>>
>> *Amos Raphenya *
>> *Bioinformatics Software Developer*
>> *Department of Biochemistry & Biomedical Sciences*
>> *McMaster University, MDCL **2317*
>> *p: (905) 525-9140 **ext: **22787*
>> *a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1*
>> *e:  raphe...@mcmaster.ca  *
>> *skype: amos_raphenya*
>>
>> ___
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>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>
>
>
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Re: [galaxy-dev] Loading or Upload Large datasets into Galaxy History

2016-01-28 Thread Nicola Soranzo 

Hi Amos,
please vote for the "Chunked file uploads" issue :)

https://github.com/galaxyproject/galaxy/issues/573

Cheers,
Nicola

On 28/01/16 19:56, Raphenya, Amogelang wrote:

Hi All,

Is there a faster way to upload or load large datasets into galaxy 
history without using FTP?


I tried /Upload_local_file/**(/to current history/)**and it doesn’t 
upload *.gz* files correctly as compared to when using*Upload_file 
*(/from your computer/).


Cheers.

/
/   
/*Amos Raphenya* /
/Bioinformatics Software Developer/
/Department of Biochemistry & Biomedical Sciences/
/McMaster University, MDCL //2317/
/p: (905) 525-9140//ext: //22787/
/a:1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1/
/e: raphe...@mcmaster.ca  /
/skype:amos_raphenya/




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Re: [galaxy-dev] Loading or Upload Large datasets into Galaxy History

2016-01-28 Thread Martin Čech 
Hi Amos,

what Galaxy are you using and where are you seeing these messages?

thanks

Martin

On Thu, Jan 28, 2016 at 2:56 PM Raphenya, Amogelang 
wrote:

> Hi All,
>
> Is there a faster way to upload or load large datasets into galaxy history
> without using FTP?
>
> I tried *Upload_local_file* (*to current history*) and it doesn’t upload
> *.gz* files correctly as compared to when using* Upload_file *(*from your
> computer*).
>
> Cheers.
>
>
> *Amos Raphenya *
> *Bioinformatics Software Developer*
> *Department of Biochemistry & Biomedical Sciences*
> *McMaster University, MDCL **2317*
> *p: (905) 525-9140 **ext: **22787*
> *a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1*
> *e:  raphe...@mcmaster.ca  *
> *skype: amos_raphenya*
>
> ___
> 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:
>   https://lists.galaxyproject.org/
>
> 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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/