Re: [galaxy-user] history

[Anton Nekrutenko]

Tanita:

Click "Options" at the top of the history pane and choose "Saved histories". 
You will see your old history listed in the middle pane.

Thanks,

anton
galaxy team


On Mar 24, 2011, at 12:15 PM, Fuchs, Tania wrote:

> Hello,
>  
> I worked on my home computer with Galaxy online and next day when I came to 
> the lab I hoped to be able to access everything I did at home through 
> history, but it does not show up in history. I was logged in both times into 
> my  account.
>  
> What did I do wrong?
>  
> Thanks!
>  
> Tania
>  
> ___
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Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org



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Re: [galaxy-user] history

[Daniel Blankenberg]

Hi Tania,

In the History pane, Click 'Options' --> 'Saved Histories' and see if your 
history is listed there.

Thanks for using Galaxy,

Dan


On Mar 24, 2011, at 12:15 PM, Fuchs, Tania wrote:

> Hello,
>  
> I worked on my home computer with Galaxy online and next day when I came to 
> the lab I hoped to be able to access everything I did at home through 
> history, but it does not show up in history. I was logged in both times into 
> my account.
>  
> What did I do wrong?
>  
> Thanks!
>  
> Tania
>  
> ___
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> Galaxy analysis and other features on the public server
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> use the Galaxy Development list:
> 
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> 
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> please use the interface at:
> 
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Re: [galaxy-user] history

[Anton Nekrutenko]

Tanita:

Histories are saved automatically, but you need to be logged in to your Galaxy 
account.

Thanks,

anton


On Mar 24, 2011, at 3:13 PM, Fuchs, Tania wrote:

> Hi Anton,
>  
> Thanks for the tip. I did not save my history, so I guess it was not saved 
> automatically, since the "saved histories" is empty. I still have everything 
> open at my home computer. Do you think I still can save it there?
>  
> Thanks a lot again for your help,
>  
> Tania
> From: Anton Nekrutenko [mailto:an...@bx.psu.edu] 
> Sent: Thursday, March 24, 2011 12:44 PM
> To: Fuchs, Tania
> Cc: galaxy-u...@bx.psu.edu
> Subject: Re: [galaxy-user] history
> 
> 
> Tanita:
> 
> Click "Options" at the top of the history pane and choose "Saved histories". 
> You will see your old history listed in the middle pane.
> 
> Thanks,
> 
> anton
> galaxy team
> 
> 
> On Mar 24, 2011, at 12:15 PM, Fuchs, Tania wrote:
> 
>> Hello,
>>  
>> I worked on my home computer with Galaxy online and next day when I came to 
>> the lab I hoped to be able to access everything I did at home through 
>> history, but it does not show up in history. I was logged in both times into 
>> my account.
>>  
>> What did I do wrong?
>>  
>> Thanks!
>>  
>> Tania
>>  
>> ___
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>> 
>>  http://lists.bx.psu.edu/listinfo/galaxy-dev
>> 
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>> 
>>  http://lists.bx.psu.edu/
> 
> Anton Nekrutenko
> http://nekrut.bx.psu.edu
> http://usegalaxy.org
> 
> 
> 

Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org



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Re: [galaxy-user] history was empty

[Ross]

Hi, Weimin,

What do you see when you select Options | Saved Histories (top right of the
history panel)?

If that doesn't show your old histories to re-open, please let us know
exactly which galaxy URL you were using and what login name you used so we
can take a look.

Note that you need to be logged in to the same user account each time for
histories to be reliably preserved between sessions.


On Tue, Dec 6, 2011 at 12:55 PM, dongdong zhaoweiming <
zhaoweiming1...@yahoo.com.cn> wrote:

> Hi,
>
> I open my galaxy and found the history was empty, I could not found my
> previous history, so how can I find it? Thanks a lot!
>
> Reards
> weimin zhao
>
> ___
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> please use the interface at:
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>



-- 
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
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Re: [galaxy-user] History not accessible

[Jennifer Jackson]

Hi Luciano,

The '228Gb' number can take some time to update, but this should be be a 
most few hours, not an entire day. To remove datasets from a history 
permanently (and remove them from disk) you will need to do two things:


1 - delete by clicking on the "X" for those datasets
2 - use 'Options -> 'Purge deleted datasets'

Within an individual history, using 'Show Hidden Datasets' is a way to 
locate datasets similar to "Show Deleted Datasets' (hidden datasets can 
be produced by workflows). Hidden datasets are often intermediate data 
that is not needed and could possibly be deleted/purged as well.


For histories, any ever created/imported by your account will be in your 
'Saved Histories' list (for now, there is no expiration date). Therese 
are automatically saved once you are logged in and do not require a 
special name.


Is isn't clear if you think one is missing or not. Do you think a 
history was deleted by accident? If so, it can be viewed under "Saved 
Histories" by using 'Advanced search' with the option 'all'. Histories 
of status 'delete' can be 'undeleted' and moved back to 'active' status, 
histories of status 'deleted permanently' cannot be recovered.


This wiki & screencast has more details:
http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets#Delete_vs_Delete_Permanently

Hopefully this helps, but please write back if you need more assistance,

Jen
Galaxy team

On 4/13/12 6:07 AM, Luciano Cosme wrote:

Hi,
  After I uploaded a couple files yesterday, I hit the storage limit
(250Gb), then I deleted 3 datasets from my history and now I can't see
anything in that history. It still says that I am using 228Gb, but I can
only access one history with ~98Gb. I try to use show deleted datasets
and it still not showing. The history that I was using disappeared. When
I use "saved datasets" I only see one history. I was logged as
ento.purch...@gmail.com 

Thank you.

Luciano


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Re: [galaxy-user] History Pane empty?

[Jennifer Jackson]

Hi Jason,

Are you still having this problem? Could you confirm that you are using 
the public Main Galaxy instance at http://main.g2.bx.psu.edu?


If so, would you help us to troubleshoot by sending back the OS and 
Browser that you are using, along with a link to a shared history (you 
can generate one from the middle pane by clicking on the down arrow at 
the right end of history name, and choosing "Share or Publish", using 
the first button). You can send the return email with your environment 
info and copied link directly to me, to keep your data private.


Sorry that you are having problems,

Jen
Galaxy team

On 11/28/12 6:51 AM, jason gagliano wrote:

Hi
I just had a quick question. My History pane to the right of my Galaxy 
account on the web suddenly was empty when I logged in. I noticed that 
I can still find all my datasets under "Saved History" or "Saved 
Datasets" but nothing will show up now in the history pane. This is 
true even when I upload a new data set.

Any thoughts on the problem and a solution?
Thanks
Jason
P.S. I have read all I could find on the topic in the help sections 
before asking this question. But I could not find anything that worked 
for me (like simply deleting cookies). I am relating this to say that 
I am trying to be a good citizen by reading first and then asking 
questions :0)



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Re: [galaxy-user] History Pane empty?

[Jennifer Jackson]

Hello Jason,

This issue was resolved on the public Main Galaxy server earlier today. 
We found that this UI behavior was often linked to the use of Internet 
Explorer as a browser. For the best UI functionality when using Galaxy, 
we recommend using Firefox, Chrome, or Safari.


Thank you for reporting the error,

Jen
Galaxy team

On 11/28/12 6:51 AM, jason gagliano wrote:

Hi
I just had a quick question. My History pane to the right of my Galaxy 
account on the web suddenly was empty when I logged in. I noticed that 
I can still find all my datasets under "Saved History" or "Saved 
Datasets" but nothing will show up now in the history pane. This is 
true even when I upload a new data set.

Any thoughts on the problem and a solution?
Thanks
Jason
P.S. I have read all I could find on the topic in the help sections 
before asking this question. But I could not find anything that worked 
for me (like simply deleting cookies). I am relating this to say that 
I am trying to be a good citizen by reading first and then asking 
questions :0)



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Re: [galaxy-user] History will not load?

[Jennifer Jackson]

Hello Maria,

The issue has been resolved. Our apologies for the inconvenience,

Jen
Galaxy team

On 9/22/13 11:55 AM, Maria Hoffman wrote:

Hello,
I have been having trouble with Galaxy since yesterday. I have been 
trying to run cuffdiff which has been waiting to run since Friday 
afternoon and now my history will not even load (red error message 
shows up).

Any incite would be much appreciated.
Maria


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Re: [galaxy-user] History will not load?

[Jennifer Jackson]

Hi Maria,

Yes, this is a known issue and we have been working on resolving it 
today. A red banner is up on the public Main server with a description. 
That said, from my own testing when you first sent this in to a test I 
just did now, there appears to be some improvement already. When fully 
cleared the banner will update.


Thank you for your patience,

Jen
Galaxy team

On 9/24/13 6:13 AM, Maria Hoffman wrote:

Hello,
Unfortunately, it appears as though the history will not load again 
this AM and the jobs I have set to run last night (cuffdiff) have not 
completed either.

Sorry to keep bothering you guys.

Maria


On Mon, Sep 23, 2013 at 2:36 PM, Jennifer Jackson > wrote:


Hello Maria,

The issue has been resolved. Our apologies for the inconvenience,

Jen
Galaxy team


On 9/22/13 11:55 AM, Maria Hoffman wrote:

Hello,
I have been having trouble with Galaxy since yesterday. I have
been trying to run cuffdiff which has been waiting to run since
Friday afternoon and now my history will not even load (red error
message shows up).
Any incite would be much appreciated.
Maria


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Re: [galaxy-user] History items remain pending (grey color)

[graham etherington (TSL)]

Hi Priya,
If you are using one of the public Galaxy servers (e.g.
http://main.g2.bx.psu.edu/), then it's quite probable that there a lots of
jobs queued in the system by other users. If your history item is grey
that means the job has been successfully submitted and is waiting its turn
in the queueing system. When the system is busy it will take longer for
the jobs to be submitted due to the high demand.
In short - give it some time, it will run eventually.
Best wishes,
Graham

Dr. Graham Etherington
Bioinformatics Support Officer,
The Sainsbury Laboratory,
Norwich Research Park,
Norwich NR4 7UH.
UK
Tel: +44 (0)1603 450601





On 25/03/2013 23:01, "Priya Bhatt"  wrote:

>Dear Galaxy Users,
>
>Forgive me in advance, but I am a VERY new Galaxy user!
>
>I am trying to go through the Galaxy 101 tutorial provided on the galaxy
>website (https://main.g2.bx.psu.edu/u/aun1/p/galaxy101).  The first step
>asks to get exon data of Chromosome 22 from UCSC database, and the second
>step asks to get the SNP data from the same database.  When I do these
>two steps, I understand the history items should turn green once they are
>processed, however after a few hours these items remain grey.  Am I doing
>something wrong?  
>
>Any help would be greatly appreciated!
>
>Thank you in advance,
>Priya
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>
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Re: [galaxy-user] History items remain pending (grey color)

[Jennifer Jackson]

  
  
Hello Priya,

Graham is correct in stating that a "grey dataset" indicates that
the job is still in the queue waiting to run. When the public server
is very busy, this delay can vary based on a few factors, but a UCSC
Table Browser data extraction is not a job that would be expected to
take very long.

That said, the public server was known to be slower later yesterday
through this morning. We are actively working to resolve this and
you should notice improvement shortly. 

I was able to get a small test job through (also a UCSC Table data
extraction) even during this time - with some delay, but not on the
order of several hours. Have your jobs completed now and were you
able to work through the exercise since first reporting the issue?
If jobs were stalled, please try again one more time and if there is
problem that continues through this afternoon, please let us know.
The exercise was designed to not be computationally intensive - and
you should be able to complete it during a single work session.

Just to let you know, sometimes it appears that jobs are waiting,
when actually all that is needed is a "History refresh" to update
the panel to show the current status. I've misinterpreted status
myself by forgetting to do this on occasion (still!). A manual
refresh certainly isn't always needed, but is worth knowing about.
There is a small double-arrow rounded icon at the top of the History
panel, to the left of the gear icon, that you can click to do the
refresh, here is a picture of it:



Hopefully this helps,

Jen
Galaxy team

On 3/25/13 4:01 PM, Priya Bhatt wrote:


  Dear Galaxy Users,

Forgive me in advance, but I am a VERY new Galaxy user!

I am trying to go through the Galaxy 101 tutorial provided on the galaxy website (https://main.g2.bx.psu.edu/u/aun1/p/galaxy101).  The first step asks to get exon data of Chromosome 22 from UCSC database, and the second step asks to get the SNP data from the same database.  When I do these two steps, I understand the history items should turn green once they are processed, however after a few hours these items remain grey.  Am I doing something wrong?  

Any help would be greatly appreciated!

Thank you in advance,
Priya
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Re: [galaxy-user] History items remain pending (grey color)

[Priya Bhatt]

Dear All,

Thank you for your prompt responses.  Yes, my jobs have processed - I guess I 
needed to be more patient! 

As far as the tutorial, it was taking much time on the version available to the 
public on the Galaxy website but I am now using an instance of Galaxy on my 
lab's network so things are moving almost instantaneously.  

 Thanks for your insight!

Best,
Priya


From: Jennifer Jackson [j...@bx.psu.edu]
Sent: Tuesday, March 26, 2013 12:14 PM
To: Priya Bhatt
Cc: galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] History items remain pending (grey color)

Hello Priya,

Graham is correct in stating that a "grey dataset" indicates that the job is 
still in the queue waiting to run. When the public server is very busy, this 
delay can vary based on a few factors, but a UCSC Table Browser data extraction 
is not a job that would be expected to take very long.

That said, the public server was known to be slower later yesterday through 
this morning. We are actively working to resolve this and you should notice 
improvement shortly.

I was able to get a small test job through (also a UCSC Table data extraction) 
even during this time - with some delay, but not on the order of several hours. 
Have your jobs completed now and were you able to work through the exercise 
since first reporting the issue? If jobs were stalled, please try again one 
more time and if there is problem that continues through this afternoon, please 
let us know. The exercise was designed to not be computationally intensive - 
and you should be able to complete it during a single work session.

Just to let you know, sometimes it appears that jobs are waiting, when actually 
all that is needed is a "History refresh" to update the panel to show the 
current status. I've misinterpreted status myself by forgetting to do this on 
occasion (still!). A manual refresh certainly isn't always needed, but is worth 
knowing about. There is a small double-arrow rounded icon at the top of the 
History panel, to the left of the gear icon, that you can click to do the 
refresh, here is a picture of it:

[cid:part1.08040502.09070800@bx.psu.edu]

Hopefully this helps,

Jen
Galaxy team

On 3/25/13 4:01 PM, Priya Bhatt wrote:

Dear Galaxy Users,

Forgive me in advance, but I am a VERY new Galaxy user!

I am trying to go through the Galaxy 101 tutorial provided on the galaxy 
website (https://main.g2.bx.psu.edu/u/aun1/p/galaxy101).  The first step asks 
to get exon data of Chromosome 22 from UCSC database, and the second step asks 
to get the SNP data from the same database.  When I do these two steps, I 
understand the history items should turn green once they are processed, however 
after a few hours these items remain grey.  Am I doing something wrong?

Any help would be greatly appreciated!

Thank you in advance,
Priya
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The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

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Re: [galaxy-user] History not updating for multiple instances of Galaxy

[Neil.Burdett]

Further, when I try "register" I add an email address and password, but the 
system still doesn't log me in

Maybe this is a database configuration issue?

I didn't think I'd need to state any specific entries in universe as I am using 
physically separate directories

i.e. /home/galaxy/galaxy-cte/ 
i.e. /home/galaxy/galaxy-Newcastle/ 

Cheers
Neil


From: Burdett, Neil (ICT Centre, Herston - RBWH)
Sent: Thursday, 21 February 2013 1:19 PM
To: galaxy-...@lists.bx.psu.edu
Cc: galaxy-user@lists.bx.psu.edu
Subject: History not updating for multiple instances of Galaxy

Hi,
I have three instances of galaxy running on the same Linux box. My 
"/etc/apache2/sites-available/default" is:

RewriteEngine on
RewriteRule ^/galaxy-csiro$ /galaxy-csiro/ [R]
RewriteRule ^/galaxy-csiro/static/style/(.*) 
/home/galaxy/galaxy-csiro/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy-csiro/static/scripts/(.*) 
/home/galaxy/galaxy-csiro/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy-csiro/static/(.*) 
/home/galaxy/galaxy-csiro/static/$1 [L]
RewriteRule ^/galaxy-csiro/favicon.ico 
/home/galaxy/galaxy-csiro/static/favicon.ico [L]
RewriteRule ^/galaxy-csiro/robots.txt 
/home/galaxy/galaxy-csiro/static/robots.txt [L]
RewriteRule ^/galaxy-csiro(.*) http://localhost:9080$1 [P]

RewriteRule ^/galaxy-cte$ /galaxy-cte/ [R]
RewriteRule ^/galaxy-cte/static/style/(.*) 
/home/galaxy/galaxy-cte/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy-cte/static/scripts/(.*) 
/home/galaxy/galaxy-cte/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy-cte/static/(.*) /home/galaxy/galaxy-cte/static/$1 
[L]
RewriteRule ^/galaxy-cte/favicon.ico 
/home/galaxy/galaxy-cte/static/favicon.ico [L]
RewriteRule ^/galaxy-cte/robots.txt 
/home/galaxy/galaxy-cte/static/robots.txt [L]
RewriteRule ^/galaxy-cte(.*) http://localhost:9000$1 [P]

RewriteRule ^/galaxy-Newcastle$ /galaxy-Newcastle/ [R]
RewriteRule ^/galaxy-Newcastle/static/style/(.*) 
/home/galaxy/galaxy-Newcastle/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy-Newcastle/static/scripts/(.*) 
/home/galaxy/galaxy-Newcastle/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy-Newcastle/static/(.*) 
/home/galaxy/galaxy-Newcastle/static/$1 [L]
RewriteRule ^/galaxy-Newcastle/favicon.ico 
/home/galaxy/galaxy-Newcastle/static/favicon.ico [L]
RewriteRule ^/galaxy-Newcastle/robots.txt 
/home/galaxy/galaxy-Newcastle/static/robots.txt [L]
RewriteRule ^/galaxy-Newcastle(.*) http://localhost:9010$1 [P]

I can view all the instances

However, when I try and "Get Data" and upload a file the history side panel 
remains empty. I can see that the files have been uploaded to (for example)

% ls -lrt galaxy-Newcastle/database/files/000/
total 22868
-rw-rw-r-- 1 galaxy galaxy 23017819 Feb 21 13:01 dataset_1.dat
-rw-rw-r-- 1 galaxy galaxy   187339 Feb 21 13:02 dataset_2.dat
-rw-rw-r-- 1 galaxy galaxy   206568 Feb 21 13:03 dataset_3.dat

Any ideas much appreciated...

The log file state:

Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342321
127.0.0.1 - - [21/Feb/2013:13:16:21 +1000] "GET 
/galaxy-Newcastle/tool_runner?tool_id=upload1 HTTP/1.1" 200 - 
"http://barium-rbh/galaxy-Newcastle/root/tool_menu"; "Mozilla/5.0 (X11; Ubuntu; 
Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0"
galaxy.web.framework DEBUG 2013-02-21 13:16:28,630 Error: this request returned 
None from get_history(): 
http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2013-02-21 13:16:28,630 Error: this request returned 
None from get_history(): 
http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned 
None from get_history(): 
http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned 
None from get_history(): 
http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned 
None from get_history(): 
http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned 
None from get_history(): 
http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create
galaxy.web.framework DEBUG 2013-02-21 13:16:28,631 Error: this request returned 
None from get_history(): 
http://barium-rbh/galaxy-Newcastle/tool_runner/upload_async_create
127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "POST 
/galaxy-Newcastle/tool_runner/upload_async_create HTTP/1.1" 500 - 
"http://barium-rbh/galaxy-Newcastle/"; "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; 
rv:18.0) Gecko/20100101 Firefox/18.0"
Debug at: http://barium-rbh/galaxy-Newcastle/_debug/view/1361342322
127.0.0.1 - - [21/Feb/2013:13:16:28 +1000] "GET