Re: [galaxy-dev] [External] Re: macs error for chipseq data

2013-01-11 Thread Dannon Baker 
The error is most likely caused by your input data and parameter choices.  If 
you click the little bug icon in the history for a dataset in the error state, 
you'll see the full error output display that will have more information and 
will hopefully help you figure out what's going on.  One potential problem 
might be that your MFOLD is too high, but we'd need to see the full error 
report to determine that.


On Jan 11, 2013, at 5:01 PM, "Sun, Wenping [USA]"  wrote:

> For the output of 1.3.7.1, I didn't check wiggle files since it takes longer 
> time. So the output are bed and html report, both with the same error and 
> that's all I have from the right panel below the file names. I already 
> deleted those errored-outputs. 
> 
> Thanks,
> Kathryn
> 
> -Original Message-
> From: Dannon Baker [mailto:dannonba...@me.com] 
> Sent: Friday, January 11, 2013 4:56 PM
> To: Sun, Wenping [USA]
> Cc: Jennifer Jackson; Galaxy Dev
> Subject: Re: [External] Re: macs error for chipseq data
> 
> 1.3.7.1 is definitely the version you want -- the Galaxy wrappers are not yet 
> compatible with 1.4* versions (so they are guaranteed to fail).  Is there 
> more error output available, or is that it, ending with #tag size?
> 
> 
> On Jan 11, 2013, at 4:48 PM, "Sun, Wenping [USA]"  wrote:
> 
>> I linked the macs version 1.3.7.1 to the default as the commands below.
>> 
>> It runs, however, still get the error message as below --
>> 
>> MACS on data 65 and data 66 (peaks: bed)
>> 0 bytes
>> An error occurred running this job: INFO @ Fri, 11 Jan 2013 19:30:50:
>> # ARGUMENTS LIST:
>> # name = MACS_in_Galaxy
>> # format = SAM
>> # ChIP-seq file = /mnt/galaxyData/files/000/dataset_66.dat
>> # control file = /mnt/galaxyData/files/000/dataset_65.dat
>> # effective genome size = 2.70e+09
>> # tag size
>> 
>> I switched to version 1.4.1 and got the error message same as the first time.
>> 
>> Thanks again,
>> Kathryn
>> 
>> -Original Message-
>> From: Dannon Baker [mailto:dannonba...@me.com]
>> Sent: Friday, January 11, 2013 12:12 PM
>> To: Jennifer Jackson
>> Cc: Galaxy Dev; Sun, Wenping [USA]
>> Subject: [External] Re: macs error for chipseq data
>> 
>> There's an issue with the MACS installation on the current cloud tools 
>> volume (which will be fixed with the next volume update coming soon).
>> 
>> For existing instances, you can get MACS working correctly by executing the 
>> following two commands (which change the default version of macs used) after 
>> ssh'ing in to your instance:
>> 
>> sudo su galaxy
>> ln -sfn /mnt/galaxyTools/tools/macs/1.3.7.1 
>> /mnt/galaxyTools/tools/macs/default
>> 
>> And that's it, no need to restart galaxy or anything.
>> 
>> -Dannon
>> 
>> On Jan 11, 2013, at 10:59 AM, Jennifer Jackson  wrote:
>> 
>>> Hi Kathryn,
>>> 
>>> I am going to post this back to the galaxy-dev list and cc Dannon so that 
>>> he or or one of the developers more experienced with troubleshooting cloud 
>>> issues can help. My guess is that there is a path problem (covered in the 
>>> first wiki link) but by no means is that the only possibility.
>>> 
>>> Thanks!
>>> Jen
>>> Galaxy team
>>> 
>>> On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
 Hi Jen,
 
 Sorry that I missed some part of your email. It is not for local galaxy 
 install. I am using the cloudman from aws and it seemed to have everything 
 for having the input files and reference genome chose. The job was shown 
 on the right panel and then the error message coming out.
 
 It seems to me that MACS was installed What is the issue?
 
 Thank you very much,
 Kathryn
>>> On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote:
 Hi Jennifer,
 
 Thanks for the information on MACS tools.
 
 Yes, I forgot to mention that I used bowtie mapped files as the input.
 
 Thank you very much,
 Kathryn
 
 
 From: Jennifer Jackson [mailto:j...@bx.psu.edu]
 Sent: Friday, January 11, 2013 3:48 AM
 To: Sun, Wenping [USA]
 Cc: galaxy-u...@bx.psu.edu
 Subject: [External] Re: [galaxy-user] macs error for chipseq data
 
 Hello Kathryn,
 
 This is occurring on your local Galaxy install? Have you installed the 
 actual MACS tool and set up the proper configuration paths? Details for 
 how to do this are in these wikis:
 http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
 http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
 
 Apart from that, I should let you know that prior to running MACS, groomed 
 fastq datasets first need to be mapped. An example can be found in our 
 Using Galaxy paper, protocol #3. Links to the paper and supplemental 
 materials (including a screencast walk-through) are available here:
 https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
 
 If you need more help with your local install, directing questions 
 to the galaxy-...@bx.psu.edu mailing list would

Re: [galaxy-dev] [External] Re: macs error for chipseq data

2013-01-11 Thread Sun, Wenping [USA] 
For the output of 1.3.7.1, I didn't check wiggle files since it takes longer 
time. So the output are bed and html report, both with the same error and 
that's all I have from the right panel below the file names. I already deleted 
those errored-outputs. 

Thanks,
Kathryn

-Original Message-
From: Dannon Baker [mailto:dannonba...@me.com] 
Sent: Friday, January 11, 2013 4:56 PM
To: Sun, Wenping [USA]
Cc: Jennifer Jackson; Galaxy Dev
Subject: Re: [External] Re: macs error for chipseq data

1.3.7.1 is definitely the version you want -- the Galaxy wrappers are not yet 
compatible with 1.4* versions (so they are guaranteed to fail).  Is there more 
error output available, or is that it, ending with #tag size?


On Jan 11, 2013, at 4:48 PM, "Sun, Wenping [USA]"  wrote:

> I linked the macs version 1.3.7.1 to the default as the commands below.
>  
> It runs, however, still get the error message as below --
>  
> MACS on data 65 and data 66 (peaks: bed)
> 0 bytes
> An error occurred running this job: INFO @ Fri, 11 Jan 2013 19:30:50:
> # ARGUMENTS LIST:
> # name = MACS_in_Galaxy
> # format = SAM
> # ChIP-seq file = /mnt/galaxyData/files/000/dataset_66.dat
> # control file = /mnt/galaxyData/files/000/dataset_65.dat
> # effective genome size = 2.70e+09
> # tag size
>  
> I switched to version 1.4.1 and got the error message same as the first time.
>  
> Thanks again,
> Kathryn
>  
> -Original Message-
> From: Dannon Baker [mailto:dannonba...@me.com]
> Sent: Friday, January 11, 2013 12:12 PM
> To: Jennifer Jackson
> Cc: Galaxy Dev; Sun, Wenping [USA]
> Subject: [External] Re: macs error for chipseq data
>  
> There's an issue with the MACS installation on the current cloud tools volume 
> (which will be fixed with the next volume update coming soon).
>  
> For existing instances, you can get MACS working correctly by executing the 
> following two commands (which change the default version of macs used) after 
> ssh'ing in to your instance:
>  
> sudo su galaxy
> ln -sfn /mnt/galaxyTools/tools/macs/1.3.7.1 
> /mnt/galaxyTools/tools/macs/default
>  
> And that's it, no need to restart galaxy or anything.
>  
> -Dannon
>  
> On Jan 11, 2013, at 10:59 AM, Jennifer Jackson  wrote:
>  
> > Hi Kathryn,
> >
> > I am going to post this back to the galaxy-dev list and cc Dannon so that 
> > he or or one of the developers more experienced with troubleshooting cloud 
> > issues can help. My guess is that there is a path problem (covered in the 
> > first wiki link) but by no means is that the only possibility.
> >
> > Thanks!
> > Jen
> > Galaxy team
> >
> > On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
> >> Hi Jen,
> >> 
> >> Sorry that I missed some part of your email. It is not for local galaxy 
> >> install. I am using the cloudman from aws and it seemed to have everything 
> >> for having the input files and reference genome chose. The job was shown 
> >> on the right panel and then the error message coming out.
> >> 
> >> It seems to me that MACS was installed What is the issue?
> >> 
> >> Thank you very much,
> >> Kathryn
> > On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote:
> >> Hi Jennifer,
> >> 
> >> Thanks for the information on MACS tools.
> >> 
> >> Yes, I forgot to mention that I used bowtie mapped files as the input.
> >> 
> >> Thank you very much,
> >> Kathryn
> >> 
> >> 
> >> From: Jennifer Jackson [mailto:j...@bx.psu.edu]
> >> Sent: Friday, January 11, 2013 3:48 AM
> >> To: Sun, Wenping [USA]
> >> Cc: galaxy-u...@bx.psu.edu
> >> Subject: [External] Re: [galaxy-user] macs error for chipseq data
> >> 
> >> Hello Kathryn,
> >>
> >> This is occurring on your local Galaxy install? Have you installed the 
> >> actual MACS tool and set up the proper configuration paths? Details for 
> >> how to do this are in these wikis:
> >> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
> >> http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
> >>
> >> Apart from that, I should let you know that prior to running MACS, groomed 
> >> fastq datasets first need to be mapped. An example can be found in our 
> >> Using Galaxy paper, protocol #3. Links to the paper and supplemental 
> >> materials (including a screencast walk-through) are available here:
> >> https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
> >>
> >> If you need more help with your local install, directing questions 
> >> to the galaxy-...@bx.psu.edu mailing list would be best,
> >>
> >> Thanks!
> >>
> >> Jen
> >> Galaxy team
> >>
> >> On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote:
> >> Dear galaxy users,
> >> 
> >> I've encountered the error while running macs on galaxy for chipseq 
> >> data. I used fastq groomed files as input and had the following 
> >> error
> >> 
> >> An error occurred running this job: /bin/sh: macs: not found
> >> 
> >> Anybody can kindly provide some hints?
> >> 
> >> Thanks,
> >> Kathryn
> >>
> >>
> >>
> >> ___
> >> The Galaxy User lis

Re: [galaxy-dev] [External] Re: macs error for chipseq data

2013-01-11 Thread Dannon Baker 
1.3.7.1 is definitely the version you want -- the Galaxy wrappers are not yet 
compatible with 1.4* versions (so they are guaranteed to fail).  Is there more 
error output available, or is that it, ending with #tag size?


On Jan 11, 2013, at 4:48 PM, "Sun, Wenping [USA]"  wrote:

> I linked the macs version 1.3.7.1 to the default as the commands below.
>  
> It runs, however, still get the error message as below --
>  
> MACS on data 65 and data 66 (peaks: bed)
> 0 bytes
> An error occurred running this job: INFO @ Fri, 11 Jan 2013 19:30:50:
> # ARGUMENTS LIST:
> # name = MACS_in_Galaxy
> # format = SAM
> # ChIP-seq file = /mnt/galaxyData/files/000/dataset_66.dat
> # control file = /mnt/galaxyData/files/000/dataset_65.dat
> # effective genome size = 2.70e+09
> # tag size
>  
> I switched to version 1.4.1 and got the error message same as the first time.
>  
> Thanks again,
> Kathryn
>  
> -Original Message-
> From: Dannon Baker [mailto:dannonba...@me.com] 
> Sent: Friday, January 11, 2013 12:12 PM
> To: Jennifer Jackson
> Cc: Galaxy Dev; Sun, Wenping [USA]
> Subject: [External] Re: macs error for chipseq data
>  
> There's an issue with the MACS installation on the current cloud tools volume 
> (which will be fixed with the next volume update coming soon).
>  
> For existing instances, you can get MACS working correctly by executing the 
> following two commands (which change the default version of macs used) after 
> ssh'ing in to your instance:
>  
> sudo su galaxy
> ln -sfn /mnt/galaxyTools/tools/macs/1.3.7.1 
> /mnt/galaxyTools/tools/macs/default
>  
> And that's it, no need to restart galaxy or anything.
>  
> -Dannon
>  
> On Jan 11, 2013, at 10:59 AM, Jennifer Jackson  wrote:
>  
> > Hi Kathryn,
> >
> > I am going to post this back to the galaxy-dev list and cc Dannon so that 
> > he or or one of the developers more experienced with troubleshooting cloud 
> > issues can help. My guess is that there is a path problem (covered in the 
> > first wiki link) but by no means is that the only possibility.
> >
> > Thanks!
> > Jen
> > Galaxy team
> >
> > On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
> >> Hi Jen,
> >> 
> >> Sorry that I missed some part of your email. It is not for local galaxy 
> >> install. I am using the cloudman from aws and it seemed to have everything 
> >> for having the input files and reference genome chose. The job was shown 
> >> on the right panel and then the error message coming out.
> >> 
> >> It seems to me that MACS was installed…. What is the issue?
> >> 
> >> Thank you very much,
> >> Kathryn
> > On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote:
> >> Hi Jennifer,
> >> 
> >> Thanks for the information on MACS tools.
> >> 
> >> Yes, I forgot to mention that I used bowtie mapped files as the input.
> >> 
> >> Thank you very much,
> >> Kathryn
> >> 
> >> 
> >> From: Jennifer Jackson [mailto:j...@bx.psu.edu]
> >> Sent: Friday, January 11, 2013 3:48 AM
> >> To: Sun, Wenping [USA]
> >> Cc: galaxy-u...@bx.psu.edu
> >> Subject: [External] Re: [galaxy-user] macs error for chipseq data
> >> 
> >> Hello Kathryn,
> >>
> >> This is occurring on your local Galaxy install? Have you installed the 
> >> actual MACS tool and set up the proper configuration paths? Details for 
> >> how to do this are in these wikis:
> >> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
> >> http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
> >>
> >> Apart from that, I should let you know that prior to running MACS, groomed 
> >> fastq datasets first need to be mapped. An example can be found in our 
> >> Using Galaxy paper, protocol #3. Links to the paper and supplemental 
> >> materials (including a screencast walk-through) are available here:
> >> https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
> >>
> >> If you need more help with your local install, directing questions to
> >> the galaxy-...@bx.psu.edu mailing list would be best,
> >>
> >> Thanks!
> >>
> >> Jen
> >> Galaxy team
> >>
> >> On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote:
> >> Dear galaxy users,
> >> 
> >> I’ve encountered the error while running macs on galaxy for chipseq
> >> data. I used fastq groomed files as input and had the following error
> >> 
> >> An error occurred running this job: /bin/sh: macs: not found
> >> 
> >> Anybody can kindly provide some hints?
> >> 
> >> Thanks,
> >> Kathryn
> >>
> >>
> >>
> >> ___
> >> 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.

Re: [galaxy-dev] [galaxy-bugs] galaxy.genenetwork.org

2013-01-11 Thread Lei Yan 
Hi Dannon,

Thanks so much.

On Fri, Jan 11, 2013 at 1:25 PM, Dannon Baker  wrote:

> I don't see any failures in the recent logs.  Has cloudlaunch worked for
> you before?
>
Yes, but cloudlaunch worked for me only at the first time.
I tried it for test at the first time. Then I deleted it, and I would
launch a regular Galaxy instance. But it always failed after that.


> A few more questions:
>
> When did this occur?
>
This occurred in recent 2 weeks, including today.

Were you restarting an existing cluster, or starting a new one?
>
No.

Using existing keypairs or a new one?
>
Tried both.


> And, do the instances actually start even though there's no web response
> (if you look in the AWS terminal manually)?
>
I don’t think it actually start, because there is not any Galaxy instance
in the AWS ec2 console.


>
> -Dannon
>
>
> On Jan 11, 2013, at 2:08 PM, Lei Yan  wrote:
>
> > Dear all,
> >
> > Recently I tried this for several times:
> > https://main.g2.bx.psu.edu/cloudlaunch
> > But each time it just show up “Launch Pending, please be patient”, and
> then it would still not respond (please see attachment).
> > Could somebody help us for this problem?
> > If you need, I can give you our AWS secret keys.
> > Thanks so much.
> >
> >
> > Lei Yan
> > leiyan2...@gmail.com
> > UTHSC
> >
> >
> >
> > On Tue, Dec 11, 2012 at 3:13 PM, Lei Yan  wrote:
> > Dear Dannon and James,
> >
> > On Mon, Dec 10, 2012 at 8:04 AM, Dannon Baker 
> wrote:
> > >   • I installed a Cloud Galaxy instance one month ago, and a user
> reported that it still has some problems. At that time, I found that it can
> be upgraded to new version in the administration page, so I did so. But its
> log showed that it “has error”, and the service cannot start. I then tried
> to reboot the machine, but Galaxy still could not start and the service is
> not responding.
> >
> > Can you share the cloud log?  This would be the best place to look to
> find out what the errors are.
> >
> > For this Cloud Galaxy instance, I can boot it, but the Galaxy service
> could not start. So I logged in this server by SSH to get the log files
> from file system.
> > And I found a strange thing, this server doesn’t mount the three
> partitions of Galaxy (/dev/xvdg1, /dev/xvdg2, /dev/xvdg3) automatically
> when booting. I thought this should be automatically, so need I setup
> something for mounting automatically?
> > I attached the log files, and they are compressed to a zip file
> “1.log.zip”.
> >
> >
> > >   • Then I tried to build a new Cloud Galaxy, but after trying at
> least 8 times it still didn’t work. Each time, after I launched the Cloud
> Galaxy instance, even its State is "running" and the "Status Checks" is
> "2/2 checks passed”, but it would still not respond if I opened “http://
> **.amazonaws.com/cloud”; I never even get to "Welcome to Galaxy on
> the cloud".
> >
> > Can you share any more information about this?  Can you confirm that
> you're using the supported AMI, have launched with the correct security
> groups, etc?  For future reference, just using usegalaxy.org/cloudlaunchis 
> probably the easiest way to make sure you avoid any launch issues.  Are
> you able to SSH in to the instance?
> >
> > I am using ami-78a00411. I attached three other files, and they are the
> AMI I am using, the security groups I am using, and the instance
> configurations.
> > I never used this usegalaxy.org/cloudlaunch. But it looks good, and I
> will try this later.
> > Yes, I can login this instance by SSH. But I never even get to "Welcome
> to Galaxy on the cloud".
> >
> >
> >
> > > Could you please give us some suggestions or let us know who we should
> contact about this issue?
> >
> > Sending email directly to galaxy-bugs, as you have, for stuff you'd
> rather not share with the wider community is the best bet.  For anything
> that isn't sensitive, emailing galaxy-dev is useful if you're working with
> customized or local/cloud installs.
> >
> > > I cannot find any telephone number on the Galaxy community pages, and
> it would be better if I could talk to someone about the problem over the
> phone.
> >
> > Would it be helpful to chat over IRC and debug this?  See the "IRC
> Channel" information on http://wiki.galaxyproject.org/Get%20Involved.
> >
> > -Dannon
> >
> > Thanks so much for your help.
> >
> >
> > Lei Yan
> > leiyan2...@gmail.com
> > UTHSC
> > <2013-01-11 10-30-41.png>
>
>
___
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in your mail client.  To manage your subscriptions to this
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[galaxy-dev] Galaxy January 11, 2013 Distribution & News Brief

2013-01-11 Thread Jennifer Jackson 
*Galaxy January 11, 2013 Distribution & News Brief* 



*
Complete News Brief 
*


*
Highlights:*

 *

   /*GCC2013 Training Day Topic Nomination closes TODAY!*/ Read more...
   
   or see http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay

 *

   XML defined Tool shed repository dependencies
   
   introduced

 *

   Various enhancements
   
   to Tool Shed  containers,
   display of README files and SVG images, and the tool shed's
   functional test framework
   
.


 *

   New genomes
    added
   to *Main * Galaxy instance and
   rsync download.

 * Plus bug fixes and related enhancements for visualizations,
   histories, workflows, and tools.

*
http://getgalaxy.org*

*http://bitbucket.org/galaxy/galaxy-dist*

*http://galaxy-dist.readthedocs.org*


new: $ hg clone http://www.bx.psu.edu/hg/galaxy galaxy-dist
upgrade: $ hg pull -u -r a4113cc1cb5e

/
*Thanks for using Galaxy,*
/

The Galaxy Team 


--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

___
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/

Re: [galaxy-dev] [External] Re: macs error for chipseq data

2013-01-11 Thread Sun, Wenping [USA] 
I linked the macs version 1.3.7.1 to the default as the commands below.



It runs, however, still get the error message as below --



MACS on data 65 and data 66 (peaks: bed)

0 bytes

An error occurred running this job: INFO @ Fri, 11 Jan 2013 19:30:50:

# ARGUMENTS LIST:

# name = MACS_in_Galaxy

# format = SAM

# ChIP-seq file = /mnt/galaxyData/files/000/dataset_66.dat

# control file = /mnt/galaxyData/files/000/dataset_65.dat

# effective genome size = 2.70e+09

# tag size



I switched to version 1.4.1 and got the error message same as the first time.



Thanks again,

Kathryn



-Original Message-
From: Dannon Baker [mailto:dannonba...@me.com]
Sent: Friday, January 11, 2013 12:12 PM
To: Jennifer Jackson
Cc: Galaxy Dev; Sun, Wenping [USA]
Subject: [External] Re: macs error for chipseq data



There's an issue with the MACS installation on the current cloud tools volume 
(which will be fixed with the next volume update coming soon).



For existing instances, you can get MACS working correctly by executing the 
following two commands (which change the default version of macs used) after 
ssh'ing in to your instance:



sudo su galaxy

ln -sfn /mnt/galaxyTools/tools/macs/1.3.7.1 /mnt/galaxyTools/tools/macs/default



And that's it, no need to restart galaxy or anything.



-Dannon



On Jan 11, 2013, at 10:59 AM, Jennifer Jackson 
mailto:j...@bx.psu.edu>> wrote:



> Hi Kathryn,

>

> I am going to post this back to the galaxy-dev list and cc Dannon so that he 
> or or one of the developers more experienced with troubleshooting cloud 
> issues can help. My guess is that there is a path problem (covered in the 
> first wiki link) but by no means is that the only possibility.

>

> Thanks!

> Jen

> Galaxy team

>

> On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:

>> Hi Jen,

>>

>> Sorry that I missed some part of your email. It is not for local galaxy 
>> install. I am using the cloudman from aws and it seemed to have everything 
>> for having the input files and reference genome chose. The job was shown on 
>> the right panel and then the error message coming out.

>>

>> It seems to me that MACS was installed What is the issue?

>>

>> Thank you very much,

>> Kathryn

> On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote:

>> Hi Jennifer,

>>

>> Thanks for the information on MACS tools.

>>

>> Yes, I forgot to mention that I used bowtie mapped files as the input.

>>

>> Thank you very much,

>> Kathryn

>>

>>

>> From: Jennifer Jackson [mailto:j...@bx.psu.edu]

>> Sent: Friday, January 11, 2013 3:48 AM

>> To: Sun, Wenping [USA]

>> Cc: galaxy-u...@bx.psu.edu

>> Subject: [External] Re: [galaxy-user] macs error for chipseq data

>>

>> Hello Kathryn,

>>

>> This is occurring on your local Galaxy install? Have you installed the 
>> actual MACS tool and set up the proper configuration paths? Details for how 
>> to do this are in these wikis:

>> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies

>> http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

>>

>> Apart from that, I should let you know that prior to running MACS, groomed 
>> fastq datasets first need to be mapped. An example can be found in our Using 
>> Galaxy paper, protocol #3. Links to the paper and supplemental materials 
>> (including a screencast walk-through) are available here:

>> https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012

>>

>> If you need more help with your local install, directing questions to

>> the galaxy-...@bx.psu.edu mailing list would 
>> be best,

>>

>> Thanks!

>>

>> Jen

>> Galaxy team

>>

>> On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote:

>> Dear galaxy users,

>>

>> I've encountered the error while running macs on galaxy for chipseq

>> data. I used fastq groomed files as input and had the following error

>>

>> An error occurred running this job: /bin/sh: macs: not found

>>

>> Anybody can kindly provide some hints?

>>

>> Thanks,

>> Kathryn

>>

>>

>>

>> ___

>> 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/

>>

>>

>> --

>> Jennifer Hillman-Jackson

>> Galaxy Support and Training

>> http://galaxyproject.org

>

> --

> Jennifer Hillman-Jackson

> Galaxy Support and Training

>

> http://galaxyproject.org


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[galaxy-dev] Bug in handling user job limits

2013-01-11 Thread Lance Parsons 
I submitted a trello "ticket" [(https://trello.com/c/6vxkqdjT) regarding 
this, but wanted to make sure I brought it to someone's attention (it's 
causing me some queue issues with my instance of galaxy).


When registered_user_job_limit and anonymous_user_job_limit are set in 
universe.wsgi jobs cannot be run, instead the following error occurs:


galaxy.jobs.handler ERROR 2012-12-04 12:44:51,869 failure running job 22396
Traceback (most recent call last):
  File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", 
line 183, in __monitor_step

job_state = self.__check_if_ready_to_run( job )
  File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", 
line 253, in __check_if_ready_to_run

state = self.__check_user_jobs( job )
  File "/data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py", 
line 274, in __check_user_jobs

if not self.user_job_count:
AttributeError: 'JobHandlerQueue' object has no attribute 'user_job_count'

Commenting out the lines for registered_user_job_limit and 
anonymous_user_job_limit in universe.wsgi allows job to be queue one again.
It looks like this is due to the fact that 
`self.__clear_user_job_count()` on line 159 of `handler.py` is only 
called when jobs are tracked in the database. If jobs are not tracked in 
the database (as in my case), the error occurs. Perhaps the fix would be 
to simply move the call outside the `if` block.


It appears this was broken in the 2012-11-13 revision (73e05bc).


--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University


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Re: [galaxy-dev] Blank local reference - even after following NGS

2013-01-11 Thread Jorge Sepulveda 
I got it! Stupid mistake of relying on the editor to add tabs to the 
> hg19hg19hg19~/ngs/refgenomes/hg19/bwa_indexed/hg19 
statement, while it was replacing each tab with 4 spaces. Now all is working 
fine!

> --
> 
> Message: 13
> Date: Wed, 9 Jan 2013 14:31:52 -0500
> From: Jorge Sepulveda 
> To: galaxy-dev@lists.bx.psu.edu
> Subject: [galaxy-dev] Blank local reference - even after following NGS
>   installation instructions
> Message-ID: <8ab4a885-98c8-4d44-b51f-cfcd2bd56...@columbia.edu>
> Content-Type: text/plain; charset=us-ascii
> 
> Hi,
> 
> I set up a local galaxy in my MacPro on 1/3/2013 using:
> hg clone https://bitbucket.org/galaxy/galaxy-dist/
> 
> into this directory:
> ~/ngs/applications/galaxy-dist
> 
> Indexed hg19.fa using bwa index to ~/ngs/refgenomes/hg19/bwa_indexed/
>   -rw-r--r--1  JSstaff  6597  Jan  2  
> 15:03  hg19.fa.amb
>   -rw-r--r--1  JSstaff  6844  Jan  2  
> 15:03  hg19.fa.ann
>   -rw-r--r--1  JSstaff  3101804844  Jan  2  15:02 
>  hg19.fa.bwt
>   -rw-r--r--1  JSstaff  775451186Jan  2  15:03
>   hg19.fa.pac
>   -rw-r--r--1  JSstaff  1550902424  Jan  2  15:06 
>  hg19.fa.sa
> 
> Added:
> hg19hg19hg19~/ngs/refgenomes/hg19/bwa_indexed/hg19 
> to this file:
> ~/ngs/applications/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/bwa_wrappers/ffa8aaa14f7c/bwa_wrappers/tool-data/bwa_index.loc
> 
> BWA shows up on the galaxy tools list, but the local reference genome box 
> remains empty. It runs fine when I use a reference sequence (chr22.fa) from 
> history.
> 
> If I download bwa (or bowtie2) and install according to the steps in 
> http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup I have the same 
> problem (empty local reference).
> 
> What am I missing?
> 
> Jorge Sepulveda, MD, PhD
> Associate Director for Laboratory Medicine,
> Medical Director of Laboratory Informatics,
> Columbia University Medical Center
> Associate Professor,
> Department of Pathology & Cell Biology
> Columbia University College of Physicians and Surgeons
> PH1590B
> 622 W 168 St
> New York, NY 10032
> Cell: (917) 862-6050
> Office: 212-305-6360
> E-mail:jls2...@columbia.edu
> 
> 
> 


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Re: [galaxy-dev] [galaxy-bugs] galaxy.genenetwork.org

2013-01-11 Thread Dannon Baker 
I don't see any failures in the recent logs.  Has cloudlaunch worked for you 
before?

A few more questions:

When did this occur?
Were you restarting an existing cluster, or starting a new one?
Using existing keypairs or a new one?
And, do the instances actually start even though there's no web response (if 
you look in the AWS terminal manually)?

-Dannon


On Jan 11, 2013, at 2:08 PM, Lei Yan  wrote:

> Dear all,
> 
> Recently I tried this for several times:
> https://main.g2.bx.psu.edu/cloudlaunch
> But each time it just show up “Launch Pending, please be patient”, and then 
> it would still not respond (please see attachment).
> Could somebody help us for this problem?
> If you need, I can give you our AWS secret keys.
> Thanks so much.
> 
> 
> Lei Yan
> leiyan2...@gmail.com
> UTHSC
> 
> 
> 
> On Tue, Dec 11, 2012 at 3:13 PM, Lei Yan  wrote:
> Dear Dannon and James,
> 
> On Mon, Dec 10, 2012 at 8:04 AM, Dannon Baker  wrote:
> >   • I installed a Cloud Galaxy instance one month ago, and a user 
> > reported that it still has some problems. At that time, I found that it can 
> > be upgraded to new version in the administration page, so I did so. But its 
> > log showed that it “has error”, and the service cannot start. I then tried 
> > to reboot the machine, but Galaxy still could not start and the service is 
> > not responding.
> 
> Can you share the cloud log?  This would be the best place to look to find 
> out what the errors are.
> 
> For this Cloud Galaxy instance, I can boot it, but the Galaxy service could 
> not start. So I logged in this server by SSH to get the log files from file 
> system.
> And I found a strange thing, this server doesn’t mount the three partitions 
> of Galaxy (/dev/xvdg1, /dev/xvdg2, /dev/xvdg3) automatically when booting. I 
> thought this should be automatically, so need I setup something for mounting 
> automatically?
> I attached the log files, and they are compressed to a zip file “1.log.zip”.
>  
> 
> >   • Then I tried to build a new Cloud Galaxy, but after trying at least 
> > 8 times it still didn’t work. Each time, after I launched the Cloud Galaxy 
> > instance, even its State is "running" and the "Status Checks" is "2/2 
> > checks passed”, but it would still not respond if I opened 
> > “http://**.amazonaws.com/cloud”; I never even get to "Welcome to Galaxy 
> > on the cloud".
> 
> Can you share any more information about this?  Can you confirm that you're 
> using the supported AMI, have launched with the correct security groups, etc? 
>  For future reference, just using usegalaxy.org/cloudlaunch is probably the 
> easiest way to make sure you avoid any launch issues.  Are you able to SSH in 
> to the instance?
> 
> I am using ami-78a00411. I attached three other files, and they are the AMI I 
> am using, the security groups I am using, and the instance configurations.
> I never used this usegalaxy.org/cloudlaunch. But it looks good, and I will 
> try this later.
> Yes, I can login this instance by SSH. But I never even get to "Welcome to 
> Galaxy on the cloud".
>  
> 
> 
> > Could you please give us some suggestions or let us know who we should 
> > contact about this issue?
> 
> Sending email directly to galaxy-bugs, as you have, for stuff you'd rather 
> not share with the wider community is the best bet.  For anything that isn't 
> sensitive, emailing galaxy-dev is useful if you're working with customized or 
> local/cloud installs.
> 
> > I cannot find any telephone number on the Galaxy community pages, and it 
> > would be better if I could talk to someone about the problem over the phone.
> 
> Would it be helpful to chat over IRC and debug this?  See the "IRC Channel" 
> information on http://wiki.galaxyproject.org/Get%20Involved.
> 
> -Dannon
> 
> Thanks so much for your help.
> 
> 
> Lei Yan
> leiyan2...@gmail.com
> UTHSC
> <2013-01-11 10-30-41.png>


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Re: [galaxy-dev] macs error for chipseq data

2013-01-11 Thread Dannon Baker 
There's an issue with the MACS installation on the current cloud tools volume 
(which will be fixed with the next volume update coming soon).

For existing instances, you can get MACS working correctly by executing the 
following two commands (which change the default version of macs used) after 
ssh'ing in to your instance:

sudo su galaxy
ln -sfn /mnt/galaxyTools/tools/macs/1.3.7.1 /mnt/galaxyTools/tools/macs/default

And that's it, no need to restart galaxy or anything.

-Dannon

On Jan 11, 2013, at 10:59 AM, Jennifer Jackson  wrote:

> Hi Kathryn,
> 
> I am going to post this back to the galaxy-dev list and cc Dannon so that he 
> or or one of the developers more experienced with troubleshooting cloud 
> issues can help. My guess is that there is a path problem (covered in the 
> first wiki link) but by no means is that the only possibility.
> 
> Thanks!
> Jen
> Galaxy team
> 
> On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
>> Hi Jen,
>>  
>> Sorry that I missed some part of your email. It is not for local galaxy 
>> install. I am using the cloudman from aws and it seemed to have everything 
>> for having the input files and reference genome chose. The job was shown on 
>> the right panel and then the error message coming out.
>>  
>> It seems to me that MACS was installed…. What is the issue?
>>  
>> Thank you very much,
>> Kathryn
> On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote:
>> Hi Jennifer,
>>  
>> Thanks for the information on MACS tools.
>>  
>> Yes, I forgot to mention that I used bowtie mapped files as the input.
>>  
>> Thank you very much,
>> Kathryn
>>  
>>  
>> From: Jennifer Jackson [mailto:j...@bx.psu.edu] 
>> Sent: Friday, January 11, 2013 3:48 AM
>> To: Sun, Wenping [USA]
>> Cc: galaxy-u...@bx.psu.edu
>> Subject: [External] Re: [galaxy-user] macs error for chipseq data
>>  
>> Hello Kathryn,
>> 
>> This is occurring on your local Galaxy install? Have you installed the 
>> actual MACS tool and set up the proper configuration paths? Details for how 
>> to do this are in these wikis:
>> http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
>> http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
>> 
>> Apart from that, I should let you know that prior to running MACS, groomed 
>> fastq datasets first need to be mapped. An example can be found in our Using 
>> Galaxy paper, protocol #3. Links to the paper and supplemental materials 
>> (including a screencast walk-through) are available here:
>> https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
>> 
>> If you need more help with your local install, directing questions to the 
>> galaxy-...@bx.psu.edu mailing list would be best,
>> 
>> Thanks!
>> 
>> Jen
>> Galaxy team
>> 
>> On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote:
>> Dear galaxy users,
>>  
>> I’ve encountered the error while running macs on galaxy for chipseq data. I 
>> used fastq groomed files as input and had the following error
>>  
>> An error occurred running this job: /bin/sh: macs: not found
>>  
>> Anybody can kindly provide some hints?
>>  
>> Thanks,
>> Kathryn
>> 
>> 
>> 
>> ___
>> 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/
>> 
>> 
>> -- 
>> Jennifer Hillman-Jackson
>> Galaxy Support and Training
>> http://galaxyproject.org
> 
> -- 
> Jennifer Hillman-Jackson
> Galaxy Support and Training
> 
> http://galaxyproject.org


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[galaxy-dev] number of jobs waiting

2013-01-11 Thread Jordi Vaquero 
Hello, 
I am trying to get an estimated time of job execution. For this reason I need 
to get the number of jobs waiting in the queue. There is any api I could use ( 
external to galaxy) in order to 
check the galaxy queue and get the number of jobs waiting to be executed? 
I have been looking for this information but I didn't find anything clear. 

Thanks for your help


Jordi


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[galaxy-dev] workflow loading error in galaxy cloudman

2013-01-11 Thread Sun, Wenping [USA] 
Dear Galaxy group,

I am uploading the double-ended NGS workflow 
(Galaxy-Workflow-mt_analysis_0.01_strand-specific_(fastq_double).ga from galaxy 
website) to galaxy cloudman and had the following error --

Workflow mt analysis 0.01 strand-specific (fastq double) (imported from 
uploaded file) imported successfully. The workflow requires the following tools 
that are not available in this Galaxy instance.You can likely install the 
required tools from one of the Galaxy tool sheds listed below.
Tool name Map with BWA, id bwa_wrapper, version 1.0.3

Galaxy main tool 
shed
Galaxy test tool 
shed

And when I tried to edit the workflow, it takes forever to load the workflow 
editor,  with "unrecognized Tool: bwa_wrapper" on the background. Does anyone 
encounter the same problem?

I really appreciate your inputs and comments,
Kathryn

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[galaxy-dev] macs error for chipseq data

2013-01-11 Thread Jennifer Jackson 

Hi Kathryn,

I am going to post this back to the galaxy-dev list and cc Dannon so 
that he or or one of the developers more experienced with 
troubleshooting cloud issues can help. My guess is that there is a path 
problem (covered in the first wiki link) but by no means is that the 
only possibility.


Thanks!
Jen
Galaxy team

On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:


Hi Jen,

Sorry that I missed some part of your email. It is not for local 
galaxy install. I am using the cloudman from aws and it seemed to have 
everything for having the input files and reference genome chose. The 
job was shown on the right panel and then the error message coming out.


It seems to me that MACS was installed What is the issue?

Thank you very much,

Kathryn


On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote:


Hi Jennifer,

Thanks for the information on MACS tools.

Yes, I forgot to mention that I used bowtie mapped files as the input.

Thank you very much,

Kathryn

**

*From:*Jennifer Jackson [mailto:j...@bx.psu.edu]
*Sent:* Friday, January 11, 2013 3:48 AM
*To:* Sun, Wenping [USA]
*Cc:* galaxy-u...@bx.psu.edu
*Subject:* [External] Re: [galaxy-user] macs error for chipseq data

Hello Kathryn,

This is occurring on your local Galaxy install? Have you installed the 
actual MACS tool and set up the proper configuration paths? Details 
for how to do this are in these wikis:

http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies

Apart from that, I should let you know that prior to running MACS, 
groomed fastq datasets first need to be mapped. An example can be 
found in our Using Galaxy paper, protocol #3. Links to the paper and 
supplemental materials (including a screencast walk-through) are 
available here:

https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012

If you need more help with your local install, directing questions to 
the galaxy-...@bx.psu.edu  mailing list 
would be best,


Thanks!

Jen
Galaxy team

On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote:

Dear galaxy users,

I've encountered the error while running macs on galaxy for
chipseq data. I used fastq groomed files as input and had the
following error

An error occurred running this job: //bin/sh: macs: not found/

//

Anybody can kindly provide some hints?

Thanks,

Kathryn




___

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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,

please use the interface at:

  


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--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org


--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

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Re: [galaxy-dev] DRMAA runner weirdness

2013-01-11 Thread Liisa Koski 
Hello,
Can you please post the link to this patch? I do not see it in the mail 
thread and I too have noticed some issues with the DRMAA job running since 
updating to the Oct. 23rd distribution. I don't know if it is related yet 
but I'd like to try the patch to see. I have two local instances of Galaxy 
(prod and dev). On my dev instance (which is fully up to date), when I run 
the same job multiple times, sometimes it finishes and sometimes it dies, 
this is independent of which node it runs on. My prod instance is still at 
the Oct. 03 distribution and does not experience this problem. So I am 
afraid to update our production instance. 

Thanks in advance,
Liisa




From:   Kyle Ellrott 
To: Nate Coraor 
Cc: "galaxy-dev@lists.bx.psu.edu" 
Date:   10/01/2013 07:44 PM
Subject:Re: [galaxy-dev] DRMAA runner weirdness
Sent by:galaxy-dev-boun...@lists.bx.psu.edu



I did a merge of galaxy-central that included the patch you posted 
today. The scheduling problem seems to have gone away. Although I'm still 
getting back 'Job output not returned from cluster' for errors. This seems 
odd, as the system previously would output stderr correctly.

Kyle


On Thu, Jan 10, 2013 at 8:30 AM, Nate Coraor  wrote:
On Jan 9, 2013, at 12:18 AM, Kyle Ellrott wrote:

> I'm running a test Galaxy system on a cluster (merged galaxy-dist on 
Janurary 4th). And I've noticed some odd behavior from the DRMAA job 
runner.
> I'm running a multithread system, one web server, one job_manager, and 
three job_handlers. DRMAA is the default job runner (the command for 
tophat2 is drmaa://-V -l mem_total=7G -pe smp 2/), with SGE 6.2u5 being 
the engine underneath.
>
> My test involves trying to run three different Tophat2 jobs. The first 
two seem to start up (and get put on the SGE queue), but the third stays 
grey, with the job manager listing it in state 'new' with command line 
'None'. It doesn't seem to leave this state. Both of the jobs that 
actually got onto the queue die (reasons unknown, but much to early, 
probably some tophat/bowtie problem), but one job is listed in error state 
with stderr as 'Job output not returned from cluster', while the other job 
(which is no longer in the SGE queue) is still listed as running.

Hi Kyle,

It sounds like there are bunch of issues here.  Do you have any limits set 
as to the number of concurrent jobs allowed?  If not, you may need to add 
a bit of debugging information to the manager or handler code to figure 
out why the 'new' job is not being dispatched for execution.

For the 'error' job, more information about output collection should be 
available from the Galaxy server log.  If you have general SGE problems 
this may not be Galaxy's fault.  You do need to make sure that the 
stdout/stderr files are able to be properly copied back to the Galaxy 
server upon job completion.

For the 'running' job, make sure you've got 'set_metadata_externally = 
True' in your Galaxy config.

--nate

>
> Any ideas?
>
>
> Kyle
> ___
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Re: [galaxy-dev] Server stops itself

2013-01-11 Thread Nate Coraor 
On Jan 11, 2013, at 4:49 AM, Rémy Dernat wrote:

> Hi Nate,
> 
> Could you push these patch on the galaxy-dist repository ?

Hi Rémy,

Unfortunately, this change just missed the cutoff for today's galaxy-dist, so 
it will have to wait for the next one, which should be in two weeks.  You are 
welcome to pull directly from galaxy-central, if you'd like.

--nate

> 
> Thanks,
> 
> Regards
> 2013/1/11 Rémy Dernat 
> Hi Nate,
> 
> Could you push these patch on the galaxy-dist repository ?
> 
> Thanks,
> 
> Regards
> 
> 
> ___
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Re: [galaxy-dev] Server stops itself

2013-01-11 Thread Rémy Dernat 
Hi Nate,

Could you push these patch on the galaxy-dist repository ?

Thanks,

Regards
2013/1/11 Rémy Dernat 

> Hi Nate,
>
> Could you push these patch on the galaxy-dist repository ?
>
> Thanks,
>
> Regards
>
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Re: [galaxy-dev] Server stops itself

2013-01-11 Thread MONJEAUD 

Hi Nate,

thank you for your answers and your speed!

Cheers,
Cyril

On 01/10/2013 06:26 PM, Nate Coraor wrote:

On Jan 10, 2013, at 4:43 AM, MONJEAUD wrote:


Hi,

indeed, you are right. In the database, the "job_runner_external_id" column is 
empty for all jobs causing the crash of Galaxy when they are stopped. I tried to launch 
the instance without the --daemon option and I have got this segmentation fault as you 
suspected:


run.sh: line 77: 19622 Segmentation fault  (core dumped) 
/local/python/2.7-bis/bin/python ./scripts/paster.py serve universe_wsgi.ini

If I understand, we can't delete a job with the state "new" (associated with an empty 
"job_runner_external_id" column)?

Hi Cyril,

This was due to a bug, which has been fixed in c015b82b3944.

--nate


Thanks,
Cyril



On 01/09/2013 07:51 PM, Nate Coraor wrote:

Hi Cyril,

If you start the server in the foreground (no --daemon option), is there a 
segfault when the process dies?  If so, this is most likely a problem where a 
job is attempting to be stopped that does not have an external job ID set.  
Could you check this in the database for one of the jobs that's causing this 
(e.g. 3065)?

Thanks,
--nate

On Jan 9, 2013, at 4:39 AM, MONJEAUD wrote:


Hello All,

after more researchs, I found that the crash of the galaxy server was caused by 
stopping jobs. We are working with our own SGE cluster.

It's weird because we can kill jobs via history or administration panel without 
problem.

In the paster.log, we just got this message before the crash of the server :

galaxy.jobs.handler DEBUG 2013-01-08 16:52:39,877 Stopping job 3065:
galaxy.jobs.handler DEBUG 2013-01-08 16:52:39,877 stopping job 3065 in drmaa 
runner

I think this problem comes when there is many jobs in "running", "new" and 
"queued" states.

Cheers,
Cyril


On 01/08/2013 04:11 PM, MONJEAUD wrote:

Hello All,

I'm trying to deploy my instance of Galaxy in production. Some tests we've done 
show that when the number of person connected is high (>20 together), the 
server stops itself.

Sometimes, I have this error in the paster.log:


Exception happened during processing of request from ('127.0.0.1', 60575)
Traceback (most recent call last):
  File "/opt/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpserver.py", line 
1053, in process_request_in_thread
self.finish_request(request, client_address)
  File "/local/python/2.7-bis/lib/python2.7/SocketServer.py", line 323, in 
finish_request
self.RequestHandlerClass(request, client_address, self)
  File "/local/python/2.7-bis/lib/python2.7/SocketServer.py", line 641, in 
__init__
self.finish()
  File "/local/python/2.7-bis/lib/python2.7/SocketServer.py", line 694, in 
finish
self.wfile.flush()
  File "/local/python/2.7-bis/lib/python2.7/socket.py", line 301, in flush
self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe

Do you have any ideas about this and how resolve it?

Cheers!!
Cyril


--

Cyril Monjeaud
Equipe Symbiose / Plate-forme GenOuest
Bureau D156
IRISA-INRIA, Campus de Beaulieu
35042 Rennes cedex, France
Tél: +33 (0) 2 99 84 74 17

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--

Cyril Monjeaud
Equipe Symbiose / Plate-forme GenOuest
Bureau D156
IRISA-INRIA, Campus de Beaulieu
35042 Rennes cedex, France
Tél: +33 (0) 2 99 84 74 17




--

Cyril Monjeaud
Equipe Symbiose / Plate-forme GenOuest
Bureau D156
IRISA-INRIA, Campus de Beaulieu
35042 Rennes cedex, France
Tél: +33 (0) 2 99 84 74 17

___
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/