Problem downloading large processed datasets : galaxy local instance
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
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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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 <hrh@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/
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 <hrh@fmi.ch <mailto:hrh@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/>
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 <hrh@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 <hrh@fmi.ch <mailto:hrh@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/>
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 <hrh@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/
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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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 <hrh@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/
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.berner@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-bounces@lists.bx.psu.edu [mailto: galaxy-dev-bounces@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 <hrh@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/
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#Dis... Thanks for using Galaxy, Dan On Apr 3, 2014, at 5:12 AM, Nilaksha Neththikumara <nilakshafreezon@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.berner@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-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@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 <hrh@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 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/
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 <dan@bx.psu.edu> 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#Dis...
Thanks for using Galaxy,
Dan
On Apr 3, 2014, at 5:12 AM, Nilaksha Neththikumara < nilakshafreezon@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.berner@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-bounces@lists.bx.psu.edu [mailto: galaxy-dev-bounces@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 <hrh@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 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/
participants (5)
-
Berner, Thomas -
Björn Grüning -
Daniel Blankenberg -
Hans-Rudolf Hotz -
Nilaksha Neththikumara