Problem downloading large processed datasets : galaxy local instance

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Problem downloading large processed datasets : galaxy local instance

Nilaksha Neththikumara
Hello all,

I'm currently successfully running a pipeline for metagenomic analysis on my locally installed galaxy instance and everything seemed to good by far. But when I'm trying to download my processed blast xml output (I used blast+ wrappers for this) , by clicking the small disk button nothing happens. I tried several options.
1) clicked the 'disk' icon to initiate the downloading
2) right clicked the 'disk' icon and tried to use saved linked as, but a dialog box doesnot appear for saving
3) tried copying the link and used curl on bash terminal, but progress bar is stuck at 0%.

I think this is happening because my blast output dataset is much larger (around ~10GB) , but if that's the case, how am I supposed to get the data out of galaxy any way??

Thank a lot in advance.

Regards!
Nilaksha

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Re: Problem downloading large processed datasets : galaxy local instance

Hans-Rudolf Hotz
Hi Nilaksha

Use the "!" icon (View details) to get the full path to the data set,
and the use 'cp' or 'scp' (if not on the same host) on your terminal.


Hope this helps, Hans-Rudolf


On 04/03/2014 07:27 AM, Nilaksha Neththikumara wrote:

> Hello all,
>
> I'm currently successfully running a pipeline for metagenomic analysis
> on my locally installed galaxy instance and everything seemed to good by
> far. But when I'm trying to download my processed blast xml output (I
> used blast+ wrappers for this) , by clicking the small disk button
> nothing happens. I tried several options.
> 1) clicked the 'disk' icon to initiate the downloading
> 2) right clicked the 'disk' icon and tried to use saved linked as, but a
> dialog box doesnot appear for saving
> 3) tried copying the link and used curl on bash terminal, but progress
> bar is stuck at 0%.
>
> I think this is happening because my blast output dataset is much larger
> (around ~10GB) , but if that's the case, how am I supposed to get the
> data out of galaxy any way??
>
> Thank a lot in advance.
>
> Regards!
> Nilaksha
>
>
> ___________________________________________________________
> 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:
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Re: Problem downloading large processed datasets : galaxy local instance

Nilaksha Neththikumara
Hi, 
Thanks a lot for the answer. But I'm afraid that detail panel does not give me the path to the dataset. Have you encountered this problem before?

Nilaksha


On Thu, Apr 3, 2014 at 12:26 PM, Hans-Rudolf Hotz <[hidden email]> wrote:
Hi Nilaksha

Use the "!" icon (View details) to get the full path to the data set, and the use 'cp' or 'scp' (if not on the same host) on your terminal.


Hope this helps, Hans-Rudolf



On 04/03/2014 07:27 AM, Nilaksha Neththikumara wrote:
Hello all,

I'm currently successfully running a pipeline for metagenomic analysis
on my locally installed galaxy instance and everything seemed to good by
far. But when I'm trying to download my processed blast xml output (I
used blast+ wrappers for this) , by clicking the small disk button
nothing happens. I tried several options.
1) clicked the 'disk' icon to initiate the downloading
2) right clicked the 'disk' icon and tried to use saved linked as, but a
dialog box doesnot appear for saving
3) tried copying the link and used curl on bash terminal, but progress
bar is stuck at 0%.

I think this is happening because my blast output dataset is much larger
(around ~10GB) , but if that's the case, how am I supposed to get the
data out of galaxy any way??

Thank a lot in advance.

Regards!
Nilaksha


___________________________________________________________
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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in your mail client.  To manage your subscriptions to this
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Re: Problem downloading large processed datasets : galaxy local instance

Hans-Rudolf Hotz
This might be due to different version of Galaxy. Is the "Job
Command-Line" listed? - Depending on the tool, you might find the path
there.

Hans-Rudolf



:Do you have the will also find the path in the "job command

On 04/03/2014 09:03 AM, Nilaksha Neththikumara wrote:

> Hi,
> Thanks a lot for the answer. But I'm afraid that detail panel does not
> give me the path to the dataset. Have you encountered this problem before?
>
> Nilaksha
>
>
> On Thu, Apr 3, 2014 at 12:26 PM, Hans-Rudolf Hotz <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Hi Nilaksha
>
>     Use the "!" icon (View details) to get the full path to the data
>     set, and the use 'cp' or 'scp' (if not on the same host) on your
>     terminal.
>
>
>     Hope this helps, Hans-Rudolf
>
>
>
>     On 04/03/2014 07:27 AM, Nilaksha Neththikumara wrote:
>
>         Hello all,
>
>         I'm currently successfully running a pipeline for metagenomic
>         analysis
>         on my locally installed galaxy instance and everything seemed to
>         good by
>         far. But when I'm trying to download my processed blast xml
>         output (I
>         used blast+ wrappers for this) , by clicking the small disk button
>         nothing happens. I tried several options.
>         1) clicked the 'disk' icon to initiate the downloading
>         2) right clicked the 'disk' icon and tried to use saved linked
>         as, but a
>         dialog box doesnot appear for saving
>         3) tried copying the link and used curl on bash terminal, but
>         progress
>         bar is stuck at 0%.
>
>         I think this is happening because my blast output dataset is
>         much larger
>         (around ~10GB) , but if that's the case, how am I supposed to
>         get the
>         data out of galaxy any way??
>
>         Thank a lot in advance.
>
>         Regards!
>         Nilaksha
>
>
>         _____________________________________________________________
>         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/
>         <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/

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Re: Problem downloading large processed datasets : galaxy local instance

Björn Grüning-3
In reply to this post by Nilaksha Neththikumara
Hi Nilaksha,

unfortunately you only see the path if you are an admin. Can you get
admin right? Otherwise, maybe downloading via the API would an alternative.

Cheers,
Bjoern

Am 03.04.2014 09:03, schrieb Nilaksha Neththikumara:

> Hi,
> Thanks a lot for the answer. But I'm afraid that detail panel does not give
> me the path to the dataset. Have you encountered this problem before?
>
> Nilaksha
>
>
> On Thu, Apr 3, 2014 at 12:26 PM, Hans-Rudolf Hotz <[hidden email]> wrote:
>
>> Hi Nilaksha
>>
>> Use the "!" icon (View details) to get the full path to the data set, and
>> the use 'cp' or 'scp' (if not on the same host) on your terminal.
>>
>>
>> Hope this helps, Hans-Rudolf
>>
>>
>>
>> On 04/03/2014 07:27 AM, Nilaksha Neththikumara wrote:
>>
>>> Hello all,
>>>
>>> I'm currently successfully running a pipeline for metagenomic analysis
>>> on my locally installed galaxy instance and everything seemed to good by
>>> far. But when I'm trying to download my processed blast xml output (I
>>> used blast+ wrappers for this) , by clicking the small disk button
>>> nothing happens. I tried several options.
>>> 1) clicked the 'disk' icon to initiate the downloading
>>> 2) right clicked the 'disk' icon and tried to use saved linked as, but a
>>> dialog box doesnot appear for saving
>>> 3) tried copying the link and used curl on bash terminal, but progress
>>> bar is stuck at 0%.
>>>
>>> I think this is happening because my blast output dataset is much larger
>>> (around ~10GB) , but if that's the case, how am I supposed to get the
>>> data out of galaxy any way??
>>>
>>> Thank a lot in advance.
>>>
>>> Regards!
>>> Nilaksha
>>>
>>>
>>> ___________________________________________________________
>>> 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/
>
___________________________________________________________
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:
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Re: Problem downloading large processed datasets : galaxy local instance

Nilaksha Neththikumara
In reply to this post by Hans-Rudolf Hotz
No, It's not. Btw do you think this problem is causing due to the capacity of the dataset.? have you experienced this before?

Thanking you,
Nilaksha


On Thu, Apr 3, 2014 at 12:43 PM, Hans-Rudolf Hotz <[hidden email]> wrote:
This might be due to different version of Galaxy. Is the "Job Command-Line" listed? - Depending on the tool, you might find the path there.

Hans-Rudolf



:Do you have the will also find the path in the "job command


On 04/03/2014 09:03 AM, Nilaksha Neththikumara wrote:
Hi,
Thanks a lot for the answer. But I'm afraid that detail panel does not
give me the path to the dataset. Have you encountered this problem before?

Nilaksha


On Thu, Apr 3, 2014 at 12:26 PM, Hans-Rudolf Hotz <[hidden email]
<mailto:[hidden email]>> wrote:

    Hi Nilaksha

    Use the "!" icon (View details) to get the full path to the data
    set, and the use 'cp' or 'scp' (if not on the same host) on your
    terminal.


    Hope this helps, Hans-Rudolf



    On 04/03/2014 07:27 AM, Nilaksha Neththikumara wrote:

        Hello all,

        I'm currently successfully running a pipeline for metagenomic
        analysis
        on my locally installed galaxy instance and everything seemed to
        good by
        far. But when I'm trying to download my processed blast xml
        output (I
        used blast+ wrappers for this) , by clicking the small disk button
        nothing happens. I tried several options.
        1) clicked the 'disk' icon to initiate the downloading
        2) right clicked the 'disk' icon and tried to use saved linked
        as, but a
        dialog box doesnot appear for saving
        3) tried copying the link and used curl on bash terminal, but
        progress
        bar is stuck at 0%.

        I think this is happening because my blast output dataset is
        much larger
        (around ~10GB) , but if that's the case, how am I supposed to
        get the
        data out of galaxy any way??

        Thank a lot in advance.

        Regards!
        Nilaksha


        _____________________________________________________________

        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/
        <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/

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Re: Problem downloading large processed datasets : galaxy local instance

Thomas
In reply to this post by Björn Grüning-3
If you can't get admin right maybe your admin will set the following option in your universe.ini on True:

# This option allows users to see the full path of datasets via the "View
# Details" option in the history.  Administrators can always see this.
#expose_dataset_path = False


Greetings, Thomas


-----Ursprüngliche Nachricht-----
Von: [hidden email] [mailto:[hidden email]] Im Auftrag von Björn Grüning
Gesendet: Donnerstag, 3. April 2014 09:13
An: [hidden email]
Betreff: Re: [galaxy-dev] Problem downloading large processed datasets : galaxy local instance

Hi Nilaksha,

unfortunately you only see the path if you are an admin. Can you get admin right? Otherwise, maybe downloading via the API would an alternative.

Cheers,
Bjoern

Am 03.04.2014 09:03, schrieb Nilaksha Neththikumara:

> Hi,
> Thanks a lot for the answer. But I'm afraid that detail panel does not
> give me the path to the dataset. Have you encountered this problem before?
>
> Nilaksha
>
>
> On Thu, Apr 3, 2014 at 12:26 PM, Hans-Rudolf Hotz <[hidden email]> wrote:
>
>> Hi Nilaksha
>>
>> Use the "!" icon (View details) to get the full path to the data set,
>> and the use 'cp' or 'scp' (if not on the same host) on your terminal.
>>
>>
>> Hope this helps, Hans-Rudolf
>>
>>
>>
>> On 04/03/2014 07:27 AM, Nilaksha Neththikumara wrote:
>>
>>> Hello all,
>>>
>>> I'm currently successfully running a pipeline for metagenomic
>>> analysis on my locally installed galaxy instance and everything
>>> seemed to good by far. But when I'm trying to download my processed
>>> blast xml output (I used blast+ wrappers for this) , by clicking the
>>> small disk button nothing happens. I tried several options.
>>> 1) clicked the 'disk' icon to initiate the downloading
>>> 2) right clicked the 'disk' icon and tried to use saved linked as,
>>> but a dialog box doesnot appear for saving
>>> 3) tried copying the link and used curl on bash terminal, but
>>> progress bar is stuck at 0%.
>>>
>>> I think this is happening because my blast output dataset is much
>>> larger (around ~10GB) , but if that's the case, how am I supposed to
>>> get the data out of galaxy any way??
>>>
>>> Thank a lot in advance.
>>>
>>> Regards!
>>> Nilaksha
>>>
>>>
>>> ___________________________________________________________
>>> 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/
>
___________________________________________________________
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:
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To search Galaxy mailing lists use the unified search at:
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Re: Problem downloading large processed datasets : galaxy local instance

Nilaksha Neththikumara
Thanks for the tip. I got admin privileges by creating an admin account, now I can see the full path. So that it basically means, we can't download larger files directly through the browser window but only from tracing the path and copying the file to some other place.  Isn't it :)


On Thu, Apr 3, 2014 at 2:21 PM, Berner, Thomas <[hidden email]> wrote:
If you can't get admin right maybe your admin will set the following option in your universe.ini on True:

# This option allows users to see the full path of datasets via the "View
# Details" option in the history.  Administrators can always see this.
#expose_dataset_path = False


Greetings, Thomas


-----Ursprüngliche Nachricht-----
Von: [hidden email] [mailto:[hidden email]] Im Auftrag von Björn Grüning
Gesendet: Donnerstag, 3. April 2014 09:13
An: [hidden email]
Betreff: Re: [galaxy-dev] Problem downloading large processed datasets : galaxy local instance

Hi Nilaksha,

unfortunately you only see the path if you are an admin. Can you get admin right? Otherwise, maybe downloading via the API would an alternative.

Cheers,
Bjoern

Am 03.04.2014 09:03, schrieb Nilaksha Neththikumara:
> Hi,
> Thanks a lot for the answer. But I'm afraid that detail panel does not
> give me the path to the dataset. Have you encountered this problem before?
>
> Nilaksha
>
>
> On Thu, Apr 3, 2014 at 12:26 PM, Hans-Rudolf Hotz <[hidden email]> wrote:
>
>> Hi Nilaksha
>>
>> Use the "!" icon (View details) to get the full path to the data set,
>> and the use 'cp' or 'scp' (if not on the same host) on your terminal.
>>
>>
>> Hope this helps, Hans-Rudolf
>>
>>
>>
>> On 04/03/2014 07:27 AM, Nilaksha Neththikumara wrote:
>>
>>> Hello all,
>>>
>>> I'm currently successfully running a pipeline for metagenomic
>>> analysis on my locally installed galaxy instance and everything
>>> seemed to good by far. But when I'm trying to download my processed
>>> blast xml output (I used blast+ wrappers for this) , by clicking the
>>> small disk button nothing happens. I tried several options.
>>> 1) clicked the 'disk' icon to initiate the downloading
>>> 2) right clicked the 'disk' icon and tried to use saved linked as,
>>> but a dialog box doesnot appear for saving
>>> 3) tried copying the link and used curl on bash terminal, but
>>> progress bar is stuck at 0%.
>>>
>>> I think this is happening because my blast output dataset is much
>>> larger (around ~10GB) , but if that's the case, how am I supposed to
>>> get the data out of galaxy any way??
>>>
>>> Thank a lot in advance.
>>>
>>> Regards!
>>> Nilaksha
>>>
>>>
>>> ___________________________________________________________
>>> 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/
>
___________________________________________________________
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:
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Re: Problem downloading large processed datasets : galaxy local instance

Daniel Blankenberg
Hi Nilaksha,

You should be able to download a file of any size in your browser from Galaxy. Can you try disabling the developer settings in your universe_wsgi.ini file and see if that helps? Info for doing that is here: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Disable_the_developer_settings


Thanks for using Galaxy,

Dan


On Apr 3, 2014, at 5:12 AM, Nilaksha Neththikumara <[hidden email]> wrote:

Thanks for the tip. I got admin privileges by creating an admin account, now I can see the full path. So that it basically means, we can't download larger files directly through the browser window but only from tracing the path and copying the file to some other place.  Isn't it :)


On Thu, Apr 3, 2014 at 2:21 PM, Berner, Thomas <[hidden email]> wrote:
If you can't get admin right maybe your admin will set the following option in your universe.ini on True:

# This option allows users to see the full path of datasets via the "View
# Details" option in the history.  Administrators can always see this.
#expose_dataset_path = False


Greetings, Thomas


-----Ursprüngliche Nachricht-----
Von: [hidden email] [mailto:[hidden email]] Im Auftrag von Björn Grüning
Gesendet: Donnerstag, 3. April 2014 09:13
An: [hidden email]
Betreff: Re: [galaxy-dev] Problem downloading large processed datasets : galaxy local instance

Hi Nilaksha,

unfortunately you only see the path if you are an admin. Can you get admin right? Otherwise, maybe downloading via the API would an alternative.

Cheers,
Bjoern

Am 03.04.2014 09:03, schrieb Nilaksha Neththikumara:
> Hi,
> Thanks a lot for the answer. But I'm afraid that detail panel does not
> give me the path to the dataset. Have you encountered this problem before?
>
> Nilaksha
>
>
> On Thu, Apr 3, 2014 at 12:26 PM, Hans-Rudolf Hotz <[hidden email]> wrote:
>
>> Hi Nilaksha
>>
>> Use the "!" icon (View details) to get the full path to the data set,
>> and the use 'cp' or 'scp' (if not on the same host) on your terminal.
>>
>>
>> Hope this helps, Hans-Rudolf
>>
>>
>>
>> On 04/03/2014 07:27 AM, Nilaksha Neththikumara wrote:
>>
>>> Hello all,
>>>
>>> I'm currently successfully running a pipeline for metagenomic
>>> analysis on my locally installed galaxy instance and everything
>>> seemed to good by far. But when I'm trying to download my processed
>>> blast xml output (I used blast+ wrappers for this) , by clicking the
>>> small disk button nothing happens. I tried several options.
>>> 1) clicked the 'disk' icon to initiate the downloading
>>> 2) right clicked the 'disk' icon and tried to use saved linked as,
>>> but a dialog box doesnot appear for saving
>>> 3) tried copying the link and used curl on bash terminal, but
>>> progress bar is stuck at 0%.
>>>
>>> I think this is happening because my blast output dataset is much
>>> larger (around ~10GB) , but if that's the case, how am I supposed to
>>> get the data out of galaxy any way??
>>>
>>> Thank a lot in advance.
>>>
>>> Regards!
>>> Nilaksha
>>>
>>>
>>> ___________________________________________________________
>>> 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/
>
___________________________________________________________
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/


___________________________________________________________
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:
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Re: Problem downloading large processed datasets : galaxy local instance

Nilaksha Neththikumara
Hey that did the trick :) Now it is smoothly downloading. Many thanks for the support all of you !

Thanks a lot
Nilaksha


On Thu, Apr 3, 2014 at 6:16 PM, Daniel Blankenberg <[hidden email]> wrote:
Hi Nilaksha,

You should be able to download a file of any size in your browser from Galaxy. Can you try disabling the developer settings in your universe_wsgi.ini file and see if that helps? Info for doing that is here: https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Disable_the_developer_settings


Thanks for using Galaxy,

Dan


On Apr 3, 2014, at 5:12 AM, Nilaksha Neththikumara <[hidden email]> wrote:

Thanks for the tip. I got admin privileges by creating an admin account, now I can see the full path. So that it basically means, we can't download larger files directly through the browser window but only from tracing the path and copying the file to some other place.  Isn't it :)


On Thu, Apr 3, 2014 at 2:21 PM, Berner, Thomas <[hidden email]> wrote:
If you can't get admin right maybe your admin will set the following option in your universe.ini on True:

# This option allows users to see the full path of datasets via the "View
# Details" option in the history.  Administrators can always see this.
#expose_dataset_path = False


Greetings, Thomas


-----Ursprüngliche Nachricht-----
Von: [hidden email] [mailto:[hidden email]] Im Auftrag von Björn Grüning
Gesendet: Donnerstag, 3. April 2014 09:13
An: [hidden email]
Betreff: Re: [galaxy-dev] Problem downloading large processed datasets : galaxy local instance

Hi Nilaksha,

unfortunately you only see the path if you are an admin. Can you get admin right? Otherwise, maybe downloading via the API would an alternative.

Cheers,
Bjoern

Am 03.04.2014 09:03, schrieb Nilaksha Neththikumara:
> Hi,
> Thanks a lot for the answer. But I'm afraid that detail panel does not
> give me the path to the dataset. Have you encountered this problem before?
>
> Nilaksha
>
>
> On Thu, Apr 3, 2014 at 12:26 PM, Hans-Rudolf Hotz <[hidden email]> wrote:
>
>> Hi Nilaksha
>>
>> Use the "!" icon (View details) to get the full path to the data set,
>> and the use 'cp' or 'scp' (if not on the same host) on your terminal.
>>
>>
>> Hope this helps, Hans-Rudolf
>>
>>
>>
>> On 04/03/2014 07:27 AM, Nilaksha Neththikumara wrote:
>>
>>> Hello all,
>>>
>>> I'm currently successfully running a pipeline for metagenomic
>>> analysis on my locally installed galaxy instance and everything
>>> seemed to good by far. But when I'm trying to download my processed
>>> blast xml output (I used blast+ wrappers for this) , by clicking the
>>> small disk button nothing happens. I tried several options.
>>> 1) clicked the 'disk' icon to initiate the downloading
>>> 2) right clicked the 'disk' icon and tried to use saved linked as,
>>> but a dialog box doesnot appear for saving
>>> 3) tried copying the link and used curl on bash terminal, but
>>> progress bar is stuck at 0%.
>>>
>>> I think this is happening because my blast output dataset is much
>>> larger (around ~10GB) , but if that's the case, how am I supposed to
>>> get the data out of galaxy any way??
>>>
>>> Thank a lot in advance.
>>>
>>> Regards!
>>> Nilaksha
>>>
>>>
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>
>
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