Re: [galaxy-user] Teaching GALAXY

2012-11-12 Thread Reiter, Larry T
I'm out of town till Tuesday.

Lawrence T Reiter, PhD
UTHSC, Memphis, TN

On Nov 9, 2012, at 4:40 PM, Lei Yan 
leiyan2...@gmail.commailto:leiyan2...@gmail.com wrote:

Dear Dannon,
We appreciate your helps.
It looks like jobs can run now. But I found a strange thing here, and I don’t 
know it is an error or not, please see attachments (marked with a red arrow).
Would you please help us to check it? Thanks again.


Dear Larry,
Does the cloud galaxy work for you now?


Lei Yan
leiyan2...@gmail.commailto:leiyan2...@gmail.com
UTHSC



On Fri, Nov 9, 2012 at 12:01 PM, Dannon Baker 
dannonba...@me.commailto:dannonba...@me.com wrote:
Lei -

It looks like you have two worker nodes, but both are currently listed as 
non-idle, yet have low load.  My guess is that something has gone wrong with 
the SGE configuration causing jobs to simply wait in the queue.  If you look at 
the contents of qconf and qstat on the admin page, does it look like there are 
jobs backed up and/or worker nodes processing the queue?  Depending on how 
comfortable you are working with SGE, it might be easiest to just click 
restart for SGE in the admin panel and see if everything goes back to normal.

-Dannon


On Nov 8, 2012, at 12:43 PM, Lei Yan 
leiyan2...@gmail.commailto:leiyan2...@gmail.com wrote:

 Dear Dannon,

 My name is Lei Yan, and I am a systems administrator at UTHSC.
 I installed a Cloud Galaxy on the Amazon EC2 about two months ago, and most 
 functions work well at that time.
 http://galaxycloud.genenetwork.org/
 But from the day before yesterday, jobs were hung up always. In my opinion, I 
 didn’t find any reasons, because all look correct from Galaxy Admin page (see 
 attachments please).
 Would you please help us to check it? I can give you the administrator 
 password if you need.
 Thanks so much.


 Lei Yan
 leiyan2...@gmail.commailto:leiyan2...@gmail.com
 UTHSC



 On Wed, Nov 7, 2012 at 4:07 PM, Larry Reiter 
 lrei...@uthsc.edumailto:lrei...@uthsc.edu wrote:
 Dannon,

 Maybe you can, but not through me.  I'm just a lowly user and biologist.  You 
 would have to contact the guy who did the installation and runs the server: 
 Lei Yan (leiyan2...@gmail.commailto:leiyan2...@gmail.com)

 I would think he would be receptive to some help, so you should mail him.

 LTR

 On 11/7/12 4:05 PM, Dannon Baker wrote:
 Main will complete the jobs eventually, though obviously that's not 
 particularly useful in the context of your class today.  How is your cloud 
 instance set up?  Cloud or local instances should be the best and most 
 reliable option for teaching with and I'd definitely like to figure out why 
 yours failed.

 -Dannon


 On Nov 7, 2012, at 3:57 PM, Larry Reiter
 lrei...@uthsc.edumailto:lrei...@uthsc.edu
  wrote:


 Dannon,

 Thanks for getting back to me.  Both the local cloud install and the main 
 server are frozen.  Well, not exactly frozen.  I can still rename or delete 
 jobs, etc.  I can even switch histories and such, but I can't get it to run 
 even simple jobs - like taking a demo file and running Fastq Groomer.  I 
 realize the load is high today on the main server, but we were able to get 
 jobs to run right up until we tried to MAP using Bowtie for Illumina.  At 
 that point, all members of the class - and me - could not go any further 
 (i.e. jobs are grey and never start to run).  Class ended almost three 
 hours ago.

 Does this help?

 LTR

 On 11/7/12 2:52 PM, Dannon Baker wrote:

 Can you describe more about what is broken with your cloud install?

 Regarding main - the server has been under heavy load today and, while it 
 shouldn't remain frozen, might be slow to dispatch and, depending on the 
 type, execute) jobs.

 -Dannon

 On Nov 7, 2012, at 1:12 PM, Larry Reiter

 lrei...@uthsc.edumailto:lrei...@uthsc.edu

  wrote:



 Tried to teach a class today on ChipSeq analysis, but the local Cloud 
 install is broken and then the Penn server froze on us.  Is there 
 something I should know?

 LTR

 --
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163


 901-448-2635tel:901-448-2635
  (Office)

 901-448-7440tel:901-448-7440
  (FAX)

 901-448-7443tel:901-448-7443
  (Lab)
 e-mail:

 lrei...@uthsc.edumailto:lrei...@uthsc.edu



 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study
 ___
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 Galaxy analysis and other features on the public server
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 .  Please keep all replies on the list by
 using reply all in your mail client.  For discussion of
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 please use the interface at:



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 --
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 

Re: [galaxy-user] Teaching GALAXY

2012-11-09 Thread Larry Reiter

Dannon,

Maybe you can, but not through me.  I'm just a lowly user and 
biologist.  You would have to contact the guy who did the installation 
and runs the server: Lei Yan (leiyan2...@gmail.com)


I would think he would be receptive to some help, so you should mail him.

LTR

On 11/7/12 4:05 PM, Dannon Baker wrote:

Main will complete the jobs eventually, though obviously that's not 
particularly useful in the context of your class today.  How is your cloud 
instance set up?  Cloud or local instances should be the best and most reliable 
option for teaching with and I'd definitely like to figure out why yours failed.

-Dannon


On Nov 7, 2012, at 3:57 PM, Larry Reiter lrei...@uthsc.edu wrote:


Dannon,

Thanks for getting back to me.  Both the local cloud install and the main 
server are frozen.  Well, not exactly frozen.  I can still rename or delete 
jobs, etc.  I can even switch histories and such, but I can't get it to run 
even simple jobs - like taking a demo file and running Fastq Groomer.  I 
realize the load is high today on the main server, but we were able to get jobs 
to run right up until we tried to MAP using Bowtie for Illumina.  At that 
point, all members of the class - and me - could not go any further (i.e. jobs 
are grey and never start to run).  Class ended almost three hours ago.

Does this help?

LTR

On 11/7/12 2:52 PM, Dannon Baker wrote:

Can you describe more about what is broken with your cloud install?

Regarding main - the server has been under heavy load today and, while it 
shouldn't remain frozen, might be slow to dispatch and, depending on the type, 
execute) jobs.

-Dannon

On Nov 7, 2012, at 1:12 PM, Larry Reiter
lrei...@uthsc.edu
  wrote:



Tried to teach a class today on ChipSeq analysis, but the local Cloud install 
is broken and then the Penn server froze on us.  Is there something I should 
know?

LTR

--
Lawrence T. Reiter, Ph.D.
Associate Professor, Department of Neurology
855 Monroe Ave., Link 415
Memphis, TN 38163

901-448-2635 (Office)
901-448-7440 (FAX)
901-448-7443 (Lab)
e-mail:
lrei...@uthsc.edu


Reiter Faculty Page
Reiter Citation Index
Tooth Study
___
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Galaxy analysis and other features on the public server
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using reply all in your mail client.  For discussion of
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use the Galaxy Development list:

  
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--
Lawrence T. Reiter, Ph.D.
Associate Professor, Department of Neurology
855 Monroe Ave., Link 415
Memphis, TN 38163

901-448-2635 (Office)
901-448-7440 (FAX)
901-448-7443 (Lab)
e-mail: lrei...@uthsc.edu

Reiter Faculty Page
Reiter Citation Index
Tooth Study



--
Lawrence T. Reiter, Ph.D.
Associate Professor, Department of Neurology
855 Monroe Ave., Link 415
Memphis, TN 38163

901-448-2635 (Office)
901-448-7440 (FAX)
901-448-7443 (Lab)
e-mail: lrei...@uthsc.edu

Reiter Faculty Page http://www.uthsc.edu/neuroscience/faculty/L_Reiter.php
Reiter Citation Index 
http://scholar.google.com/citations?user=-kaQJ14Jhl=en

Tooth Study http://tinyurl.com/88f688l
___
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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

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Re: [galaxy-user] Teaching GALAXY

2012-11-09 Thread Larry Reiter
It looks like both the main server and our local install are frozen.  
Nothing has run since we started yesterday at about 11:30am.  Anybody 
know why?


LTR

On 11/7/12 4:05 PM, Dannon Baker wrote:

Main will complete the jobs eventually, though obviously that's not 
particularly useful in the context of your class today.  How is your cloud 
instance set up?  Cloud or local instances should be the best and most reliable 
option for teaching with and I'd definitely like to figure out why yours failed.

-Dannon


On Nov 7, 2012, at 3:57 PM, Larry Reiter lrei...@uthsc.edu wrote:


Dannon,

Thanks for getting back to me.  Both the local cloud install and the main 
server are frozen.  Well, not exactly frozen.  I can still rename or delete 
jobs, etc.  I can even switch histories and such, but I can't get it to run 
even simple jobs - like taking a demo file and running Fastq Groomer.  I 
realize the load is high today on the main server, but we were able to get jobs 
to run right up until we tried to MAP using Bowtie for Illumina.  At that 
point, all members of the class - and me - could not go any further (i.e. jobs 
are grey and never start to run).  Class ended almost three hours ago.

Does this help?

LTR

On 11/7/12 2:52 PM, Dannon Baker wrote:

Can you describe more about what is broken with your cloud install?

Regarding main - the server has been under heavy load today and, while it 
shouldn't remain frozen, might be slow to dispatch and, depending on the type, 
execute) jobs.

-Dannon

On Nov 7, 2012, at 1:12 PM, Larry Reiter
lrei...@uthsc.edu
  wrote:



Tried to teach a class today on ChipSeq analysis, but the local Cloud install 
is broken and then the Penn server froze on us.  Is there something I should 
know?

LTR

--
Lawrence T. Reiter, Ph.D.
Associate Professor, Department of Neurology
855 Monroe Ave., Link 415
Memphis, TN 38163

901-448-2635 (Office)
901-448-7440 (FAX)
901-448-7443 (Lab)
e-mail:
lrei...@uthsc.edu


Reiter Faculty Page
Reiter Citation Index
Tooth Study
___
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/


--
Lawrence T. Reiter, Ph.D.
Associate Professor, Department of Neurology
855 Monroe Ave., Link 415
Memphis, TN 38163

901-448-2635 (Office)
901-448-7440 (FAX)
901-448-7443 (Lab)
e-mail: lrei...@uthsc.edu

Reiter Faculty Page
Reiter Citation Index
Tooth Study



--
Lawrence T. Reiter, Ph.D.
Associate Professor, Department of Neurology
855 Monroe Ave., Link 415
Memphis, TN 38163

901-448-2635 (Office)
901-448-1160 (FAX)
901-448-7443 (Lab)
e-mail: lrei...@uthsc.edu

Reiter Faculty Page http://www.uthsc.edu/neuroscience/faculty/L_Reiter.php
Reiter Citation Index 
http://scholar.google.com/citations?user=-kaQJ14Jhl=en
___
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:

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Re: [galaxy-user] Teaching GALAXY

2012-11-09 Thread Dannon Baker
Lei -

It looks like you have two worker nodes, but both are currently listed as 
non-idle, yet have low load.  My guess is that something has gone wrong with 
the SGE configuration causing jobs to simply wait in the queue.  If you look at 
the contents of qconf and qstat on the admin page, does it look like there are 
jobs backed up and/or worker nodes processing the queue?  Depending on how 
comfortable you are working with SGE, it might be easiest to just click 
restart for SGE in the admin panel and see if everything goes back to normal.

-Dannon


On Nov 8, 2012, at 12:43 PM, Lei Yan leiyan2...@gmail.com wrote:

 Dear Dannon,
 
 My name is Lei Yan, and I am a systems administrator at UTHSC.
 I installed a Cloud Galaxy on the Amazon EC2 about two months ago, and most 
 functions work well at that time.
 http://galaxycloud.genenetwork.org/
 But from the day before yesterday, jobs were hung up always. In my opinion, I 
 didn’t find any reasons, because all look correct from Galaxy Admin page (see 
 attachments please).
 Would you please help us to check it? I can give you the administrator 
 password if you need.
 Thanks so much.
 
 
 Lei Yan
 leiyan2...@gmail.com
 UTHSC
 
 
 
 On Wed, Nov 7, 2012 at 4:07 PM, Larry Reiter lrei...@uthsc.edu wrote:
 Dannon,
 
 Maybe you can, but not through me.  I'm just a lowly user and biologist.  You 
 would have to contact the guy who did the installation and runs the server: 
 Lei Yan (leiyan2...@gmail.com)
 
 I would think he would be receptive to some help, so you should mail him.
 
 LTR
 
 On 11/7/12 4:05 PM, Dannon Baker wrote:
 Main will complete the jobs eventually, though obviously that's not 
 particularly useful in the context of your class today.  How is your cloud 
 instance set up?  Cloud or local instances should be the best and most 
 reliable option for teaching with and I'd definitely like to figure out why 
 yours failed.
 
 -Dannon
 
 
 On Nov 7, 2012, at 3:57 PM, Larry Reiter 
 lrei...@uthsc.edu
  wrote:
 
 
 Dannon,
 
 Thanks for getting back to me.  Both the local cloud install and the main 
 server are frozen.  Well, not exactly frozen.  I can still rename or delete 
 jobs, etc.  I can even switch histories and such, but I can't get it to run 
 even simple jobs - like taking a demo file and running Fastq Groomer.  I 
 realize the load is high today on the main server, but we were able to get 
 jobs to run right up until we tried to MAP using Bowtie for Illumina.  At 
 that point, all members of the class - and me - could not go any further 
 (i.e. jobs are grey and never start to run).  Class ended almost three 
 hours ago.
 
 Does this help?
 
 LTR
 
 On 11/7/12 2:52 PM, Dannon Baker wrote:
 
 Can you describe more about what is broken with your cloud install? 
 
 Regarding main - the server has been under heavy load today and, while it 
 shouldn't remain frozen, might be slow to dispatch and, depending on the 
 type, execute) jobs.
 
 -Dannon
 
 On Nov 7, 2012, at 1:12 PM, Larry Reiter 
 
 lrei...@uthsc.edu
 
  wrote:
 
 
 
 Tried to teach a class today on ChipSeq analysis, but the local Cloud 
 install is broken and then the Penn server froze on us.  Is there 
 something I should know?
 
 LTR
 
 -- 
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
 
 901-448-2635
  (Office)
 
 901-448-7440
  (FAX)
 
 901-448-7443
  (Lab)
 e-mail: 
 
 lrei...@uthsc.edu
 
 
 
 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study
 ___
 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/
 -- 
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
 
 901-448-2635
  (Office)
 
 901-448-7440
  (FAX)
 
 901-448-7443
  (Lab)
 e-mail: 
 lrei...@uthsc.edu
 
 
 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study
 
 
 
 -- 
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
 901-448-2635 (Office)
 901-448-7440 (FAX)
 901-448-7443 (Lab)
 e-mail: lrei...@uthsc.edu
 
 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study
 
 2012-11-07 13-35-01.png2012-11-07 13-36-16.png


___
The Galaxy User list should be used for the discussion of
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Re: [galaxy-user] Teaching GALAXY

2012-11-08 Thread Dannon Baker
NGS jobs are experiencing significant delays at this time due to load -- we're 
looking into it.  Regarding the local install I'd have to recommend pinging the 
administrator on site there -- they should be able to help out.

-Dannon

On Nov 8, 2012, at 10:44 AM, Larry Reiter lrei...@uthsc.edu wrote:

 It looks like both the main server and our local install are frozen.  Nothing 
 has run since we started yesterday at about 11:30am.  Anybody know why?
 
 LTR
 
 On 11/7/12 4:05 PM, Dannon Baker wrote:
 Main will complete the jobs eventually, though obviously that's not 
 particularly useful in the context of your class today.  How is your cloud 
 instance set up?  Cloud or local instances should be the best and most 
 reliable option for teaching with and I'd definitely like to figure out why 
 yours failed.
 
 -Dannon
 
 
 On Nov 7, 2012, at 3:57 PM, Larry Reiter 
 lrei...@uthsc.edu
  wrote:
 
 
 Dannon,
 
 Thanks for getting back to me.  Both the local cloud install and the main 
 server are frozen.  Well, not exactly frozen.  I can still rename or delete 
 jobs, etc.  I can even switch histories and such, but I can't get it to run 
 even simple jobs - like taking a demo file and running Fastq Groomer.  I 
 realize the load is high today on the main server, but we were able to get 
 jobs to run right up until we tried to MAP using Bowtie for Illumina.  At 
 that point, all members of the class - and me - could not go any further 
 (i.e. jobs are grey and never start to run).  Class ended almost three 
 hours ago.
 
 Does this help?
 
 LTR
 
 On 11/7/12 2:52 PM, Dannon Baker wrote:
 
 Can you describe more about what is broken with your cloud install? 
 
 Regarding main - the server has been under heavy load today and, while it 
 shouldn't remain frozen, might be slow to dispatch and, depending on the 
 type, execute) jobs.
 
 -Dannon
 
 On Nov 7, 2012, at 1:12 PM, Larry Reiter 
 
 lrei...@uthsc.edu
 
  wrote:
 
 
 
 Tried to teach a class today on ChipSeq analysis, but the local Cloud 
 install is broken and then the Penn server froze on us.  Is there 
 something I should know?
 
 LTR
 
 -- 
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
 901-448-2635 (Office)
 901-448-7440 (FAX)
 901-448-7443 (Lab)
 e-mail: 
 
 lrei...@uthsc.edu
 
 
 
 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study
 ___
 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/
 
 -- 
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
 901-448-2635 (Office)
 901-448-7440 (FAX)
 901-448-7443 (Lab)
 e-mail: 
 lrei...@uthsc.edu
 
 
 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study
 
 
 
 -- 
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
 901-448-2635 (Office)
 901-448-1160 (FAX)
 901-448-7443 (Lab)
 e-mail: lrei...@uthsc.edu
 
 Reiter Faculty Page
 Reiter Citation Index

___
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/


Re: [galaxy-user] Teaching GALAXY

2012-11-07 Thread Dannon Baker
Can you describe more about what is broken with your cloud install? 

Regarding main - the server has been under heavy load today and, while it 
shouldn't remain frozen, might be slow to dispatch and, depending on the type, 
execute) jobs.

-Dannon

On Nov 7, 2012, at 1:12 PM, Larry Reiter lrei...@uthsc.edu wrote:

 Tried to teach a class today on ChipSeq analysis, but the local Cloud install 
 is broken and then the Penn server froze on us.  Is there something I should 
 know?
 
 LTR
 
 -- 
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
 901-448-2635 (Office)
 901-448-7440 (FAX)
 901-448-7443 (Lab)
 e-mail: lrei...@uthsc.edu
 
 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study
 ___
 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/

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at usegalaxy.org.  Please keep all replies on the list by
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local Galaxy instances and the Galaxy source code, please
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Re: [galaxy-user] Teaching GALAXY

2012-11-07 Thread Larry Reiter

Dannon,

Thanks for getting back to me.  Both the local cloud install and the 
main server are frozen.  Well, not exactly frozen.  I can still rename 
or delete jobs, etc.  I can even switch histories and such, but I can't 
get it to run even simple jobs - like taking a demo file and running 
Fastq Groomer.  I realize the load is high today on the main server, but 
we were able to get jobs to run right up until we tried to MAP using 
Bowtie for Illumina.  At that point, all members of the class - and me - 
could not go any further (i.e. jobs are grey and never start to run).  
Class ended almost three hours ago.


Does this help?

LTR

On 11/7/12 2:52 PM, Dannon Baker wrote:

Can you describe more about what is broken with your cloud install?

Regarding main - the server has been under heavy load today and, while it 
shouldn't remain frozen, might be slow to dispatch and, depending on the type, 
execute) jobs.

-Dannon

On Nov 7, 2012, at 1:12 PM, Larry Reiter lrei...@uthsc.edu wrote:


Tried to teach a class today on ChipSeq analysis, but the local Cloud install 
is broken and then the Penn server froze on us.  Is there something I should 
know?

LTR

--
Lawrence T. Reiter, Ph.D.
Associate Professor, Department of Neurology
855 Monroe Ave., Link 415
Memphis, TN 38163

901-448-2635 (Office)
901-448-7440 (FAX)
901-448-7443 (Lab)
e-mail: lrei...@uthsc.edu

Reiter Faculty Page
Reiter Citation Index
Tooth Study
___
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/



--
Lawrence T. Reiter, Ph.D.
Associate Professor, Department of Neurology
855 Monroe Ave., Link 415
Memphis, TN 38163

901-448-2635 (Office)
901-448-7440 (FAX)
901-448-7443 (Lab)
e-mail: lrei...@uthsc.edu

Reiter Faculty Page http://www.uthsc.edu/neuroscience/faculty/L_Reiter.php
Reiter Citation Index 
http://scholar.google.com/citations?user=-kaQJ14Jhl=en

Tooth Study http://tinyurl.com/88f688l
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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,
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  http://lists.bx.psu.edu/

Re: [galaxy-user] Teaching GALAXY

2012-11-07 Thread Tilahun Abebe
I also had a similar issue. I thought it has to do with the hurricane in
the east coat and never bothered to ask. Even small analyses (such as
running the RNA-seq analysis exercise by Jeremy Goecks) were stalled; in a
couple of instances for a day or more.

Thanks.

Tilahun
--

On Wed, Nov 7, 2012 at 2:57 PM, Larry Reiter lrei...@uthsc.edu wrote:

  Dannon,

 Thanks for getting back to me.  Both the local cloud install and the main
 server are frozen.  Well, not exactly frozen.  I can still rename or delete
 jobs, etc.  I can even switch histories and such, but I can't get it to run
 even simple jobs - like taking a demo file and running Fastq Groomer.  I
 realize the load is high today on the main server, but we were able to get
 jobs to run right up until we tried to MAP using Bowtie for Illumina.  At
 that point, all members of the class - and me - could not go any further
 (i.e. jobs are grey and never start to run).  Class ended almost three
 hours ago.

 Does this help?

 LTR


 On 11/7/12 2:52 PM, Dannon Baker wrote:

 Can you describe more about what is broken with your cloud install?

 Regarding main - the server has been under heavy load today and, while it 
 shouldn't remain frozen, might be slow to dispatch and, depending on the 
 type, execute) jobs.

 -Dannon

 On Nov 7, 2012, at 1:12 PM, Larry Reiter lrei...@uthsc.edu 
 lrei...@uthsc.edu wrote:


  Tried to teach a class today on ChipSeq analysis, but the local Cloud 
 install is broken and then the Penn server froze on us.  Is there something I 
 should know?

 LTR

 --
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 901-448-2635 (Office)901-448-7440 (FAX)901-448-7443 (Lab)
 e-mail: lrei...@uthsc.edu

 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study
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 --
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163

 901-448-2635 (Office)
 901-448-7440 (FAX)
 901-448-7443 (Lab)
 e-mail: lrei...@uthsc.edu

 Reiter Faculty Pagehttp://www.uthsc.edu/neuroscience/faculty/L_Reiter.php
 Reiter Citation 
 Indexhttp://scholar.google.com/citations?user=-kaQJ14Jhl=en
 Tooth Study http://tinyurl.com/88f688l

 ___
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 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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 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: [galaxy-user] Teaching GALAXY

2012-11-07 Thread Dannon Baker
Main will complete the jobs eventually, though obviously that's not 
particularly useful in the context of your class today.  How is your cloud 
instance set up?  Cloud or local instances should be the best and most reliable 
option for teaching with and I'd definitely like to figure out why yours failed.

-Dannon


On Nov 7, 2012, at 3:57 PM, Larry Reiter lrei...@uthsc.edu wrote:

 Dannon,
 
 Thanks for getting back to me.  Both the local cloud install and the main 
 server are frozen.  Well, not exactly frozen.  I can still rename or delete 
 jobs, etc.  I can even switch histories and such, but I can't get it to run 
 even simple jobs - like taking a demo file and running Fastq Groomer.  I 
 realize the load is high today on the main server, but we were able to get 
 jobs to run right up until we tried to MAP using Bowtie for Illumina.  At 
 that point, all members of the class - and me - could not go any further 
 (i.e. jobs are grey and never start to run).  Class ended almost three hours 
 ago.
 
 Does this help?
 
 LTR
 
 On 11/7/12 2:52 PM, Dannon Baker wrote:
 Can you describe more about what is broken with your cloud install? 
 
 Regarding main - the server has been under heavy load today and, while it 
 shouldn't remain frozen, might be slow to dispatch and, depending on the 
 type, execute) jobs.
 
 -Dannon
 
 On Nov 7, 2012, at 1:12 PM, Larry Reiter 
 lrei...@uthsc.edu
  wrote:
 
 
 Tried to teach a class today on ChipSeq analysis, but the local Cloud 
 install is broken and then the Penn server froze on us.  Is there something 
 I should know?
 
 LTR
 
 -- 
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
 901-448-2635 (Office)
 901-448-7440 (FAX)
 901-448-7443 (Lab)
 e-mail: 
 lrei...@uthsc.edu
 
 
 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study
 ___
 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/
 
 
 -- 
 Lawrence T. Reiter, Ph.D.
 Associate Professor, Department of Neurology
 855 Monroe Ave., Link 415
 Memphis, TN 38163
 
 901-448-2635 (Office)
 901-448-7440 (FAX)
 901-448-7443 (Lab)
 e-mail: lrei...@uthsc.edu
 
 Reiter Faculty Page
 Reiter Citation Index
 Tooth Study

___
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/