Re: [galaxy-dev] Problem downloading large processed datasets : galaxy local instance

2014-04-03 Thread 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 h...@fmi.ch 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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Re: [galaxy-dev] Problem downloading large processed datasets : galaxy local instance

2014-04-03 Thread 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 h...@fmi.ch
mailto:h...@fmi.ch 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/

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http://galaxyproject.org/search/mailinglists/



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Re: [galaxy-dev] Problem downloading large processed datasets : galaxy local instance

2014-04-03 Thread Björn Grüning

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 h...@fmi.ch 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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Re: [galaxy-dev] Problem downloading large processed datasets : galaxy local instance

2014-04-03 Thread Nilaksha Neththikumara
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 h...@fmi.ch 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 h...@fmi.ch
 mailto:h...@fmi.ch 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/



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Re: [galaxy-dev] Problem downloading large processed datasets : galaxy local instance

2014-04-03 Thread 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 thomas.ber...@jki.bund.dewrote:

 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: galaxy-dev-boun...@lists.bx.psu.edu [mailto:
 galaxy-dev-boun...@lists.bx.psu.edu] Im Auftrag von Björn Grüning
 Gesendet: Donnerstag, 3. April 2014 09:13
 An: galaxy-dev@lists.bx.psu.edu
 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 h...@fmi.ch 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
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Re: [galaxy-dev] Problem downloading large processed datasets : galaxy local instance

2014-04-03 Thread 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 nilakshafree...@gmail.com 
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 thomas.ber...@jki.bund.de 
 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: galaxy-dev-boun...@lists.bx.psu.edu 
 [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Im Auftrag von Björn Grüning
 Gesendet: Donnerstag, 3. April 2014 09:13
 An: galaxy-dev@lists.bx.psu.edu
 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 h...@fmi.ch 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
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 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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