Re: [galaxy-user] Job of format conversion waiting for over 5 days

[Nate Coraor]

Hi Eduardo,

I believe the job in question is not running because one of its inputs
(#101) failed to have metadata set properly. This situation can be fixed by
using the 'auto-detect' button on the failed dataset.

--nate


On Mon, Mar 31, 2014 at 5:20 PM, Eduardo Fox  wrote:

> 2014-03-31 11:29 GMT+02:00 Eduardo Fox :
> > Hello,
> >
> > Please I would like to know if it would be normal of a job to be
> > queued for several days? It is a SAM to BAM conversion, and it has
> > been waiting for over 5 days to run. I understand that the SAM file is
> > pretty large but other similar conversions I made on the server
> > recently were done within few minutes.
> >
> > Thanks!
> >
> > --
> > Eduardo G. P. Fox
> >
> > http://eduardofox.blogspot.com.br/
> > http://www.mendeley.com/profiles/eduardo-fox/
>
>
>
> --
> Eduardo G. P. Fox
>
> http://eduardofox.blogspot.com.br/
> http://www.mendeley.com/profiles/eduardo-fox/
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Re: [galaxy-user] jobs not running

[Nate Coraor]

Hi Ruth,

The queue was very busy this morning as it would appear that someone is
using the site for a workshop or class. I've cleared out these jobs since
they were blocking regular use, and your jobs should begin running normally
shortly. Sorry for the inconvenience.

Thanks,
--nate


On Wed, Dec 4, 2013 at 8:20 AM, Ruth Eberhardt  wrote:

> Hi
>
> Apologies if this is the wrong mailing list.
> Is there a problem with jobs running on Galaxy today?
> I have jobs (MACS and FASTQC) which have been waiting to run for over 4
> hours, bit not yet started to run.
>
> Many thanks
> Ruth
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Re: [galaxy-user] SNP finding

[Nate Coraor]

Hi Mark,

This error is not tool related.  Could you click the “bug” icon to send us an 
error report?

—nate

On Nov 11, 2013, at 8:33 AM, Mark Lindsay  wrote:

> Dear Galaxy Users
> 
> I wondered if anybody is having the same problem.
> 
> I am trying to run CuffDiff using the latest version of GenCode18 and keep 
> getting the following error message.
> 
> Is there a problem with the network or is it me?
> 
> Best wishes
> 
> Mark
> 
> 
> 
> 
> 
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Re: [galaxy-user] Pb with ftp connexion (FileZilla)

[Nate Coraor]

Hi Fabrice,

Are you connecting to `usegalaxy.org`?  This changed when we moved 
main.g2.bx.psu.edu to usegalaxy.org.

Thanks,
--nate

On Nov 8, 2013, at 6:32 AM, Fabrice Besnard wrote:

> Hi,
> 
> I am trying to connect to the Galaxy server via Filezilla in order to
> upload datasets.
> The connexion fails, with this message:  "ECONNREFUSED - Connection
> refused by server".
> I have checked my password which works well to login to my account on
> the main server.
> 
> Is it just temporal?
> Should I try to reset my password and give a new try?
> 
> Thanks for assistance,
> best,
> -- 
> Fabrice Besnard
> Institute of Biology of the Ecole Normale Supérieure (IBENS)
> 46 rue d'Ulm, 75230 Paris cedex 05, France
> 8th floor. Office: Room 802. Lab: Room 817.
> mail: fbesn...@biologie.ens.fr
> Tel: +33-1-44-32-39-31
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Re: [galaxy-user] problems in transitioning from Tophat to Cuffdiff

[Nate Coraor]

This is great news, thanks for letting us know.

--nate

On Oct 22, 2013, at 2:34 PM, Elwood Linney wrote:

> thank you all, its clearly working now and that is coming just in time, the 
> results of two of these datasets will help us plan our next experiments for 
> capping up a manuscript or two
> 
> el linney
> 
> 
> On Tue, Oct 22, 2013 at 12:03 PM, Nate Coraor  wrote:
> Hi Elwood,
> 
> Jeremy and I took at a look at this.  The failures in your history with this 
> message:
> 
>   Error: number of labels must match number of conditions
> 
> ...are due to a regression in the cuffdiff tool which Jeremy has just fixed.  
> Some characters such as spaces in the condition name were valid prior to the 
> move, but after the move they became invalid.  They should now be valid once 
> again.
> 
> You've got one tophat job running and a cuffdiff job queued, and the rest of 
> your grey datasets are waiting for those two jobs to be finished before 
> they'll be queued (we'll be working on creating a visual distinction for 
> this).  I fixed the queued cuffdiff job, which I believe should allow it to 
> run without error (or at least, not the same error).
> 
> --nate
> 
> On Oct 22, 2013, at 9:56 AM, Jennifer Jackson wrote:
> 
> > Elwood,
> >
> > Would you please share:
> >
> > 1. an original history that worked (if possible)
> > 2. the workflow you are using and let me know how you generated (did you 
> > extract it recently (last week or so)?
> > 3. problem history
> >
> > There are a few known issues in here, some mitigated, one that has to do 
> > with extracted workflows from existing older histories that is Cuffdiff 
> > specific (actually, a few problems, found another last night). I want to 
> > rule those out or at least try to provide feedback.
> >
> > I am at a conference over next several days, so let's use galaxy-bugs as a 
> > cc whenever we communicate so nothing is left lingering, plus I know Nate 
> > was looking into some of your data. Jeremy may jump also in at any time and 
> > help - he is the author of the wrapper.
> >
> > So, in your reply, remove galaxy-u...@bx.psu.edu and add 
> > galaxy-b...@bx.psu.edu
> >
> > Jen
> > Galaxy team
> >
> > On 10/22/13 5:42 AM, Elwood Linney wrote:
> >>
> >> After successfully using RNAseq software in  Galaxy online for about 10 
> >> different datasets to just get gene expression differences between 
> >> replicates from control versus exposed zebrafish embryos,  I am having no 
> >> luck getting cuffdiff to work with the "moved" Galaxy.
> >>
> >> I had this problem with histories developed before the move and histories 
> >> developed after the move.
> >>
> >> I have had this problem using an order cuffmerge gtf file that worked in 
> >> the past in Cuffdiff, with a new cuffmerge file developed from cufflinks 
> >> of the files and by just using a ref file gtf from UCSC.
> >>
> >> I don't know if this is just some interface problem with a different 
> >> version of the software that was included with the move, or a reference 
> >> genome that does not interface with Cuffdiff.  It has happened with about 
> >> 5 different histories.
> >>
> >> Is anyone else having this problem? And found a solution?
> >>
> >> Elwood Linney
> >>
> >>
> >> ___
> >> 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/
> >>
> >>
> >> To search Galaxy mailing lists use the unified search at:
> >>
> >>
> >> http://galaxyproject.org/search/mailinglists/
> >
> > --
> > Jennifer Hillman-Jackson
> >
> > http://galaxyproject.org
> > ___
> > The Galaxy User list should be used for the discussion of
> > Galaxy analysis and other features

Re: [galaxy-user] problems in transitioning from Tophat to Cuffdiff

[Nate Coraor]

Hi Elwood,

Jeremy and I took at a look at this.  The failures in your history with this 
message:

  Error: number of labels must match number of conditions

...are due to a regression in the cuffdiff tool which Jeremy has just fixed.  
Some characters such as spaces in the condition name were valid prior to the 
move, but after the move they became invalid.  They should now be valid once 
again.

You've got one tophat job running and a cuffdiff job queued, and the rest of 
your grey datasets are waiting for those two jobs to be finished before they'll 
be queued (we'll be working on creating a visual distinction for this).  I 
fixed the queued cuffdiff job, which I believe should allow it to run without 
error (or at least, not the same error).

--nate

On Oct 22, 2013, at 9:56 AM, Jennifer Jackson wrote:

> Elwood,
> 
> Would you please share:
> 
> 1. an original history that worked (if possible)
> 2. the workflow you are using and let me know how you generated (did you 
> extract it recently (last week or so)?
> 3. problem history
> 
> There are a few known issues in here, some mitigated, one that has to do with 
> extracted workflows from existing older histories that is Cuffdiff specific 
> (actually, a few problems, found another last night). I want to rule those 
> out or at least try to provide feedback.
> 
> I am at a conference over next several days, so let's use galaxy-bugs as a cc 
> whenever we communicate so nothing is left lingering, plus I know Nate was 
> looking into some of your data. Jeremy may jump also in at any time and help 
> - he is the author of the wrapper.
> 
> So, in your reply, remove galaxy-u...@bx.psu.edu and add 
> galaxy-b...@bx.psu.edu
> 
> Jen
> Galaxy team
> 
> On 10/22/13 5:42 AM, Elwood Linney wrote:
>> 
>> After successfully using RNAseq software in  Galaxy online for about 10 
>> different datasets to just get gene expression differences between 
>> replicates from control versus exposed zebrafish embryos,  I am having no 
>> luck getting cuffdiff to work with the "moved" Galaxy.
>> 
>> I had this problem with histories developed before the move and histories 
>> developed after the move.
>> 
>> I have had this problem using an order cuffmerge gtf file that worked in the 
>> past in Cuffdiff, with a new cuffmerge file developed from cufflinks of the 
>> files and by just using a ref file gtf from UCSC.
>> 
>> I don't know if this is just some interface problem with a different version 
>> of the software that was included with the move, or a reference genome that 
>> does not interface with Cuffdiff.  It has happened with about 5 different 
>> histories.
>> 
>> Is anyone else having this problem? And found a solution?
>> 
>> Elwood Linney
>> 
>> 
>> ___
>> 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/
>> 
>> 
>> To search Galaxy mailing lists use the unified search at:
>> 
>>   
>> http://galaxyproject.org/search/mailinglists/
> 
> -- 
> Jennifer Hillman-Jackson
> 
> http://galaxyproject.org
> ___
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Re: [galaxy-user] Issues on RNAseq since the changeover

[Nate Coraor]

On Oct 18, 2013, at 12:48 PM, Elwood Linney wrote:

> My histories seem to be stopping their processing around the Tophat-cuffmerge 
> steps since the change over of Galaxy online. Sometimes a red box appears 
> over my history name but disappears in a minute or less.
> 
> I am wondering, given the way the Toolshed now looks different for RNAseq 
> work,  if some changes have been made that are disallowing the procedures I 
> used previously.
> 
> For example:
> 
> I run larger Fastq files (100 million to 200 million 50bp single-ended reads 
> per sample).  I have been grooming my illumina fastq's, using Tophat (not 
> Tophat2) for alignment, then Cuffmerge, then Cuffdiff.  This worked in the 
> past but my history are just getting thru Tophat or Cuffmerge and stalling.  
> Should I be doing this in a different manner?
> 
> This has been my second time around with these datasets after it was 
> suggested that I delete and start all over again.
> 
> 
> Elwood Linney

Hi Elwood,

The wait is unfortunately due to two limits on large multicore jobs like 
cuffmerge and tophat:

  - Only 1 job per user could previously be placed into the cluster queue for 
multicore jobs - as of this morning we've increased it to 2
  - All of the nodes available for running multicore jobs are currently 
allocated, so there is some wait, even once your job is allowed to be added to 
the queue

You had a tophat job running prior to increasing the limit to 2, so no other 
jobs would have even been eligible to complete until that job finished.  After 
the increase you still have the same tophat job running but another one has 
been queued, and it is waiting for available nodes.

I hope you'll find that the wait time for these is shorter than on the old 
Galaxy Main.  We are also expecting to add additional hardware to this pool 
soon.

--nate

> 
> ___
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Re: [galaxy-user] can I use GlobusOnline to transfer data to the usegalaxy server instead of ftp

[Nate Coraor]

Hi Starr,

Not currently, although we'll be looking in to setting up usegalaxy.org as a 
globus online endpoint in the near future.

--nate

On Oct 16, 2013, at 4:09 PM, Hazard, E. Starr wrote:

> Folks,
> 
> Is it possible to use globusonline (https://www.globusonline.org) to move 
> files to and from the https://usegalaxy.org  server?
> 
> Starr
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Re: [galaxy-user] Online galaxy turning everything red on RNAseq steps

[Nate Coraor]

The problem with cuffdiff should be fixed.  Still looking at the tophat 
failures.

Thanks for your patience, and for sticking with us as we iron this out.

--nate

On Oct 9, 2013, at 7:52 PM, Jennifer Jackson wrote:

> Hi Elwood,
> 
> As I emailed to your direct question, we are looking at your bug reports in 
> detail and will get back to you there. Thanks for submitting the problems 
> that way.
> 
> For anyone else reading, if you find problems right now on the upgraded 
> server, we are most definitely interested in learning about them. Please 
> submit bug reports for anything odd, even if it seems small, and put in the 
> comments additional observations if you have time.
> 
> We appreciate the feedback, and your patience, as always!
> 
> Jen
> Galaxy team
> 
> On 10/9/13 1:04 PM, Elwood Linney wrote:
>> 
>> Hello,  I have been waiting a few weeks to process some RNA seq datasets but 
>> woke up this morning with lots of   steps red.  I thought it 
>> just might be because of the movement of the system but I processed steps 
>> for some histories and everything has turned red.
>> 
>> I also noticed that online Galaxy now has RNAseq steps separated into two 
>> sections--does this have something to do with the problems?
>> 
>> el linney
>> Duke University Medical Center
>> 
>> 
>> ___
>> The Galaxy User list should be used for the discussion of
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>> 
>>   
>> http://lists.bx.psu.edu/listinfo/galaxy-dev
>> 
>> 
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>> please use the interface at:
>> 
>>   
>> http://lists.bx.psu.edu/
>> 
>> 
>> To search Galaxy mailing lists use the unified search at:
>> 
>>   
>> http://galaxyproject.org/search/mailinglists/
> 
> -- 
> Jennifer Hillman-Jackson
> 
> http://galaxyproject.org
> ___
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Re: [galaxy-user] cannot download data to Galaxy

[Nate Coraor]

On Sep 11, 2013, at 9:56 AM, Elwood Linney wrote:

> 
> Hello,
> My connection with Galaxy online shutoff last night while I was transferring 
> data to it.  When I tried to connect again with Fetch this morning I was not 
> allowed and a message like "Sorry the maximum number of clients for this user 
> are already connected."
> 
> I have had what appears to be the bad habit of not logging off to Galaxy.  I 
> am working on the same data sets with three different computers, I only have 
> one login to Galaxy, so yes, I was logged in on 3 different computers.  When 
> I logged off of them, and tried to transfer data, I still got the same 
> message.
> 
> I realize people might be trying to get around the 250gb limit by having 
> multiple logins--I am not one of them, I am the only user on the three 
> computers I am using.  If not logging off when I leave the computer is a 
> problem to Galaxy, I will religiously log off each time I am not using the 
> computer (the computers are in three different rooms in my lab and my lab 
> consists of just me and a tech--I am the only one who knows the computer 
> login for both the computers and for Galaxy).
> 
> If I have created a problem by being "lazy", I apologize, but I have grown 
> dependent upon using Galaxy online and some new data just came in.

Hi Elwood,

This is not due to staying logged in to the web interface, I believe it's a bug 
in the FTP server that we're using.  I've restarted the server, could you let 
us know if you're still getting the maximum clients message if you try to 
connect?

--nate

> 
> Sincerely,
> 
> Elwood Linney
> Professor of Molecular Genetics and Microbiology
> Duke University Medical Center
> ___
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Re: [galaxy-user] error message from Filezilla

[Nate Coraor]

On Sep 11, 2013, at 7:48 AM, Amit Pande wrote:

> Hi,
> 
> I am getting the following error from the server :
> Command:USER genebus...@googlemail.com
> Response:331 Password required for genebus...@googlemail.com
> Command:PASS ***
> Response:530 Sorry, the maximum number of clients (3) for this user are 
> already connected.
> Error:Critical error
> Error:Could not connect to server.
> 
> Can you please help.

Hi Amit,

Please give it a try now, I've restarted the FTP server (I believe this is due 
to a bug in the server).

--nate

> 
> warm regards,
> Amit.
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Re: [galaxy-user] Egg build failed for numpy 1.6.0

[Nate Coraor]

Hi,

Almost all of the Galaxy development team uses Macs, so it should certainly 
work.  The problems with eggs, as you have both found, typically come with 
using non-standard versions of Python.  Your best bet is to use the version 
that shipped with your version of OS X, which can be found in 
/System/Library/Frameworks/Python.framework.  You can ensure that this version 
is always used by putting it first on $PATH or setting up a virtualenv with it, 
e.g.:

  % virtualenv 
--python=/System/Library/Frameworks/Python.framework/Versions/2.7/bin/python 
genv

--nate

On Aug 5, 2013, at 8:12 AM, Fabrice BESNARD wrote:

> Hi,
> 
> I am preferentially using the main server. But recently I have also tried
> to build a local Galaxy server. I also have a mac (Mac Pro OSx 10.6.8).
> 
> Since I am not a specialist at all, I asked some kind of "expert" people
> from my institute. They told me that installing Galaxy on Mac can really
> be nightmare because there are some conflicts in the versions of python...
> This could explain the problem you are encountering with the egg
> dependencies.
> 
> So they advised me to install an Ubuntu (12.04) operating system in a
> virtual machine using Virtual box.
> This is supposed to be much easier to install Galaxy and indeed, the
> installation of my local galaxy server ran fast and well.
> 
> However, I don't know whether the tip is good or not, because I am now
> facing big problems with the virtual machine: the Ubuntu virtual machine
> is very unstable and often crashes while running big datas on Galaxy...
> The problem does not come from Galaxy, but from either Ubuntu guest
> system, the virtual machine or the communication with the mac host system
> and I haven't found out how to fix it yet. But since your version of Mac
> is different, you can try this solution, it might work better in your
> configuration.
> 
> Hope that helps,
> 
> Fabrice
> 
> 
> But at the moment, I have lots of problem with the
>> Hi,
>> I am trying to install a local version of galaxy on my mac book (x86_64,
> OSx 10.8.4). I seem to be having a lot of trouble with fetching and
> installing specific egg dependencies. Initially pysam was giving me
> trouble, but once I ran scramble.py -e pysam, the problem was fixed. Now
> I have trouble with the numpy egg dependency. Does anyone have any idea
>> why a egg would fail to build. I am assuming it is because I have a more
> recent numpy version (1.7.1) installed already. What should I do, short
> of
>> uninstalling the newer version of numpy ?
>> Any help on the matter would be greatly appreciated.
>> Thank you.
>> L
>> --
>> ===
>>> Dr. Lahcen Campbell<
>>> Contact: lahcencampb...@gmail.com<
>>> http://bioinf.may.ie/index.html   <
>> ===
>> ___
>> 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
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>> please use the interface at:
>>  http://lists.bx.psu.edu/
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>>  http://galaxyproject.org/search/mailinglists/
> 
> 
> -- 
> Fabrice Besnard
> Institute of Biology of the Ecole Normale Supérieure (IBENS)
> 46 rue d'Ulm, 75230 Paris cedex 05, France
> 8th floor. Office: Room 802. Lab: Room 817.
> mail: fbesn...@biologie.ens.fr
> Tel: +33-1-44-32-39-44
> 
> 
> 
> 
> ___
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> 


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Re: [galaxy-user] Galaxy server down?

[Nate Coraor]

Hi Sam,

The job queue stalled over the weekend and has been recovering as of yesterday. 
 All queued jobs should have run at this time, but if you are still 
experiencing problems, please let us know.  Sorry for the inconvenience, and 
thanks for using Galaxy.

--nate

On Aug 5, 2013, at 7:53 AM, Anto Praveen Rajkumar Rajamani wrote:

> Hello,
> 
> I am on the same boat.
> I experience similar problems.
> What is wrong with Galaxy?
> 
> Best wishes,
> Anto
> 
> 
> From: galaxy-user-boun...@lists.bx.psu.edu 
> [galaxy-user-boun...@lists.bx.psu.edu] on behalf of Elizabeth Clare 
> [elclare.evol.biol...@gmail.com]
> Sent: 04 August 2013 11:04
> To: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] Galaxy server down?
> 
> Hi,
> 
> I think Galaxy was down earlier this week - I saw several several messages 
> when trying to access the public server, but I'm still getting no function on 
> the public site. Are there still problems? 
> 
> I can load the page now, make new workflows and set tasks but no tasks have 
> been completed in a few days. For example, I set a file to upload yesterday 
> and it still has the blue working indication. Tasks from two days ago are 
> grey and "waiting to run".
> 
> Any ideas what has gone wrong?
> 
> Beth
> 
> 
> On Fri, Aug 2, 2013 at 12:18 PM, Elizabeth Clare 
>  wrote:
> Hi Jen,
> 
> I have had little response from the galaxy public server in the last two days 
> (I'm in England) (https://main.g2.bx.psu.edu). At the moment I cannot load 
> the webpage or any page associated with it. I have had messages "Internal 
> Server Error" then one about a brief shut down saying we should contact an 
> administrator if it went on for a while. It appeared to come back early this 
> morning but now is unresponsive again.
> 
> I guess I'm reporting a continual error now. Has it gone down?
> 
> Thanks,
> 
> Beth
> 
> -- 
> 
> 
> 
> Dr. Elizabeth L. Clare
> 
> School of Biological and Chemical Sciences
> Queen Mary University of London
> Mile End Road, London E1 4NS
> Room 1.02, G. E. Fogg Building
> e.cl...@qmul.ac.uk
> +44 (0)207 882 5687
> 
> http://webspace.qmul.ac.uk/eclare/
> 
> "If you say yes more often than you say no, you will do interesting things in 
> your life"
> 
> 
> 
> -- 
> 
> 
> 
> Dr. Elizabeth L. Clare
> 
> School of Biological and Chemical Sciences
> Queen Mary University of London
> Mile End Road, London E1 4NS
> Room 1.02, G. E. Fogg Building
> e.cl...@qmul.ac.uk
> +44 (0)207 882 5687
> 
> http://webspace.qmul.ac.uk/eclare/
> 
> "If you say yes more often than you say no, you will do interesting things in 
> your life"
> ___
> The Galaxy User list should be used for the discussion of
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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
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>  http://lists.bx.psu.edu/listinfo/galaxy-dev
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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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> 
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Re: [galaxy-user] [galaxy-dev] Connecting to new Galaxy Cloudman by FTP

[Nate Coraor]

On Jul 8, 2013, at 3:50 PM, Mohammad Heydarian wrote:

> Hi,
> I am having trouble setting up a FTP connection with the recently released 
> version of Galaxy Cloudman (ami-118bfc78). 
> 
> I have instantiated the new version of Galaxy Cloudman with CloudLaunch and 
> also through the AWS EC2 wizard (using the same security group settings as 
> the previous versions) and neither instance will connect to my FTP connection.
> 
> Has anyone else had this problem? Does anyone know what is preventing the FTP 
> connection? 
> 
> Any help would be greatly appreciated.

Hey Mo,

This may be a case of the new password hashing algorithm's incompatibility with 
the provided ProFTPD config.  Could you try the following:

1. Set 'use_pbkdf2 = False' in universe_wsgi.ini anywhere in the [app:main] 
section
2. Restart Galaxy
3. Reset your password in the Galaxy UI
4. Test FTP again

--nate

> 
>  
> Cheers, 
> Mo Heydarian
> 
> ___
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Re: [galaxy-user] problem with registration

[Nate Coraor]

On May 28, 2013, at 5:40 AM, Patel, Bella wrote:

> Hi
> I have tried to register for Galaxy but apparantly a user with my email 
> address already exists! Very strange as I have never registered for this 
> software.
>  
> Can you advise?
>  
> Bella Patel

Hi Bella,

It's possible that your account creation request was accidentally submitted 
twice, which would have displayed the error message you received.  If you are 
unable to log in to the account using the password you specified, please use 
the password reset feature to gain access to your account.

--nate

> ___
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Re: [galaxy-user] Question about scripting

[Nate Coraor]

Hello,

I've moved this over to the galaxy-dev list since it concerns a local 
installation.

You'll want to use the 'condor' job running plugin, which is provided with the 
Galaxy distribution.  Have a look at the job_conf.xml.sample_advanced file to 
see how this would be configured.

A very basic job_conf.xml that should submit all jobs to HTCondor:











--nate

On Apr 19, 2013, at 8:32 AM, leconte wrote:

> hello,
> 
> My subject is at the border between Galaxy and Condor
> 
> I'found method to use Galaxy with condor cluster solution.
> 
> In fact I have wrote a script when Galaxy call clustalw2 , it calls in fact a 
> script called clustalw2.
> 
> All run exactly as I want excepting  ... but Galaxy get in error and said 
> there was a problem
> 
> 
> I turn my script to debug mode and it puts followings output
> 
> + prog=/usr/bin/clustalw2
> + err=0
> + infile=-infile=/home/galaxy/galaxy-dist/database/files/000/dataset_11.dat
> + 
> outfile=-outfile=/home/galaxy/galaxy-dist/database/job_working_directory/000/46/galaxy_dataset_80.dat
> + outorder=-OUTORDER=ALIGNED
> + seqnos=-SEQNOS=OFF
> + typeseq=-TYPE=DNA
> + var6=
> + var7=
> + var8=
> + var9=
> + echo
> 
> ++ echo -infile=/home/galaxy/galaxy-dist/database/files/000/dataset_11.dat
> ++ sed -e s/-infile=//
> + infile2=/home/galaxy/galaxy-dist/database/files/000/dataset_11.dat
> ++ sed -e 's/galaxy_dataset_\(.*\)\.dat//'
> ++ sed -e s/-outfile=//
> ++ echo 
> -outfile=/home/galaxy/galaxy-dist/database/job_working_directory/000/46/galaxy_dataset_80.dat
> + WorkingDir=/home/galaxy/galaxy-dist/database/job_working_directory/000/46/
> + mkdir -p /home/galaxy/galaxy-dist/database/job_working_directory/000/46/
> + mkdir -p /home/galaxy/galaxy-dist/database/job_working_directory/000/46/
> + mkdir -p /home/galaxy/galaxy-dist/database/job_working_directory/000/46/
> + [[ -n /usr/bin/clustalw2==clustalw2 ]]
> + echo 'universe= vanilla'
> + echo 'executable  = /usr/bin/mpirun '
> + echo 'arguments   = "-np 10 -hostfile /home/galaxy/hostfile 
> /usr/bin/clustalw-mpi 
> -infile=/home/galaxy/galaxy-dist/database/files/000/dataset_11.dat 
> -outfile=/home/galaxy/galaxy-dist/database/job_working_directory/000/46/galaxy_dataset_80.dat
>   -OUTORDER=ALIGNED  -SEQNOS=OFF -TYPE=DNA "'
> + echo 'Getenv  = True
> machine_count   = 1
> transfer_input_files= /home/galaxy/hostfile,/usr/bin/clustalw-mpi, 
> /home/galaxy/galaxy-dist/database/files/000/dataset_11.dat
> should_transfer_files   = yes
> Log = /home/galaxy/logs/normal.$(cluster).$(process).log
> Output  = /home/galaxy/logs/normal.$(cluster).$(process).out
> Error   = /home/galaxy/logs/normal.$(cluster).$(process).error
> notification= never
> queue 1'
> + /usr/bin/condor_submit /home/galaxy/submit
> Submitting job(s).
> 1 job(s) submitted to cluster 179.
> 
> 
> 
> 
> I suspect the method I use, doesn't return properly information to galaxy ... 
> but I don't know what I can do ...
> 
> Any Idea ...
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Re: [galaxy-user] wrong disk usage figure reported on galaxy main

[Nate Coraor]

On Mar 7, 2013, at 4:46 AM,   wrote:

> Hi,
>  
> I noticed since yesterday that my “disk usage” % (top-right) has jumped from 
> ~20% to ~ 80 % for no apparent reason.
> The added size of all my current histories is now only 29 Gb, which should be 
> ~11%, and I looked in my deleted histories but all of them are 0 bytes in 
> size and with status “deleted permanently”, there are no histories currently 
> shared with me by other users.
>  
> Is there something else I can check or look into in order to get my disk 
> usage back to where it should be ?
> Many thanks in advance for your help !

Hi Pierre,

There was an error in calculating your disk usage - it has been recalculated 
and the correct number should now be displayed.  Sorry for the inconvenience.

--nate

>  
> Pierre
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Re: [galaxy-user] Problem Loading History Pane

[Nate Coraor]

On Feb 15, 2013, at 10:35 AM, Mike Dufault wrote:

> To whom it may concern:
>  
> The History panel on the right side of the Galaxy page is taking a very very 
> long time to load. Also, when it does load, I have tired to save my .bam 
> files and the transmissions gets truncated to ~7000kb - 8000kb of data. All 
> of my .bam files are several GB.
>  
> Some times, when I retry tor download the data, it succeeds and other times 
> it is again truncated. The size of the truncation may be different for the 
> same file on the retry attempt.
>  
> Is there a problem with Galaxy?

Hi Mike,

There are some performance problems with the Main site that we are currently 
investigating.  Thanks for the information and we apologize for the problems.

--nate

>  
> Thanks,
> Mike
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Re: [galaxy-user] Problems with large gzipped fasta files

[Nate Coraor]

On Feb 13, 2013, at 12:25 PM, Jim Robinson wrote:

> Sorry Nate, I misunderstood at first, you want a URL to the dataset here on 
> my server?  I can definitely copy one up to an http server,  I still have 
> Ricardo's files on a hard disk.   I'll start the copy now and let you know 
> when its ready.

Yeah, that's it exactly.  Thanks!

--nate

> 
> Jim
> 
>> Hi Jim,
>> 
>> Could you send me a URL to the dataset so I can grab a copy and try to 
>> reproduce this problem?  Sorry for the trouble you've been having with the 
>> upload functionality and the delay in getting back to you.
>> 
>> --nate
>> 
>> On Feb 5, 2013, at 8:48 AM, Jim Robinson wrote:
> 


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Re: [galaxy-user] Problems with large gzipped fasta files

[Nate Coraor]

Hi Jim,

Could you send me a URL to the dataset so I can grab a copy and try to 
reproduce this problem?  Sorry for the trouble you've been having with the 
upload functionality and the delay in getting back to you.

--nate

On Feb 5, 2013, at 8:48 AM, Jim Robinson wrote:

> Hi,
> 
> I am having a lot of difficulty uploading some large gzipped fastqs (~ 10GB) 
> to the public server.   I have tried both ftp and "pulling" by http URL.   
> The upload succeeds, however I get an error as it tries to gunzip it.I 
> have tried more than 10 times now and succeeded once.  These files are 
> correct and complete, and gunzip properly locally.   The error shown is 
> usually this
> 
> empty
> format: txt, database: ?
> Problem decompressing gzipped data
> 
> However on 2 occasions (both ftp uploads) I got the traceback below.   Am I 
> missing some obvious trick?   I searched the archives and see references to 
> problems with large gzipped files but no solutions.
> 
> Thanks
> 
> Jim
> 
> 
> Traceback (most recent call last):
>   File "/galaxy/home/g2main/galaxy_main/tools/data_source/upload.py", line 
> 384, in 
> __main__()
>   File "/galaxy/home/g2main/galaxy_main/tools/data_source/upload.py", line 
> 373, in __main__
> add_file( dataset, registry, json_file, output_path )
>   File "/galaxy/home/g2main/galaxy_main/tools/data_source/upload.py", line 
> 270, in add_file
> line_count, converted_path = sniff.convert_newlines( dataset.path, 
> in_place=in_place )
>   File "/galaxy/home/g2main/galaxy_main/lib/galaxy/datatypes/sniff.py", line 
> 106, in convert_newlines
> shutil.move( temp_name, fname )
>   File "/usr/lib/python2.7/shutil.py", line 299, in move
> copy2(src, real_dst)
>   File "/usr/lib/python2.7/shutil.py", line 128, in copy2
> copyfile(src, dst)
>   File "/usr/lib/python2.7/shutil.py", line 84, in copyfile
> copyfileobj(fsrc, fdst)
>   File "/usr/lib/python2.7/shutil.py", line 49, in copyfileobj
> buf = fsrc.read(length)
> IOError: [Errno 5] Input/output error
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Re: [galaxy-user] Local Install - Understanding Upload File Concept

[Nate Coraor]

On Nov 16, 2012, at 12:24 PM, greg wrote:

> Also what would I look for in the log file to know if it's issuing jobs?
> 
> I started a new upload, but I don't see anything from the galaxy user
> when I run qstat.

If you follow the log, you should see messages from galaxy.jobs, and 
specifically, galaxy.jobs.runners.drmaa.

--nate

> 
> Thanks again.
> 
> Greg
> 
> On Fri, Nov 16, 2012 at 12:22 PM, greg  wrote:
>> I guess I'm still confused about new_file_path.
>> 
>> The upload tool uses that directory to store files temporariliy until
>> the upload completes?  And then moves it? (Will it clean up anything
>> placed in the new_file_path directory?)
>> 
>> Thanks,
>> 
>> Greg
>> 
>> On Fri, Nov 16, 2012 at 10:56 AM, Nate Coraor  wrote:
>>> On Nov 16, 2012, at 10:41 AM, greg wrote:
>>> 
>>>> On Fri, Nov 16, 2012 at 10:00 AM, Nate Coraor  wrote:
>>>>> On Nov 16, 2012, at 9:14 AM, greg wrote:
>>>>> 
>>>>> Are you running the upload tool on a cluster?
>>>>> 
>>>>> --nate
>>>>> 
>>>> 
>>>> Well I have Galaxy set up to send it's jobs to SGE/qsub but I haven't
>>>> verified that it's doing that yet.  I wanted to upload a file to test
>>>> on first.
>>>> 
>>>> Here are the changes I made to universe_wsgi.ini after copying the sample:
>>>> 
>>>> 
>>>>> #upload1 = local:///
>>>> 
>>> 
>>> I'm guessing that it's working, you can verify by having a look in your 
>>> Galaxy server output/log file.  new_file_path will need to be set to 
>>> something that is accessible on the cluster.
>>> 
>>> --nate
>>> 
>>>> 
>>>> -Greg
>>> 


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Re: [galaxy-user] Local Install - Understanding Upload File Concept

[Nate Coraor]

On Nov 16, 2012, at 12:22 PM, greg wrote:

> I guess I'm still confused about new_file_path.
> 
> The upload tool uses that directory to store files temporariliy until
> the upload completes?  And then moves it? (Will it clean up anything
> placed in the new_file_path directory?)

Yes, the parameters of the upload tool are written to a temp file in this 
directory.  It is cleaned up upon completion.

A lot of other things use new_file_path, and not all of them clean themselves 
up, so it's a good idea to use an automated process to clean the directory.

--nate

> 
> Thanks,
> 
> Greg
> 
> On Fri, Nov 16, 2012 at 10:56 AM, Nate Coraor  wrote:
>> On Nov 16, 2012, at 10:41 AM, greg wrote:
>> 
>>> On Fri, Nov 16, 2012 at 10:00 AM, Nate Coraor  wrote:
>>>> On Nov 16, 2012, at 9:14 AM, greg wrote:
>>>> 
>>>> Are you running the upload tool on a cluster?
>>>> 
>>>> --nate
>>>> 
>>> 
>>> Well I have Galaxy set up to send it's jobs to SGE/qsub but I haven't
>>> verified that it's doing that yet.  I wanted to upload a file to test
>>> on first.
>>> 
>>> Here are the changes I made to universe_wsgi.ini after copying the sample:
>>> 
>>> 
>>>> #upload1 = local:///
>>> 
>> 
>> I'm guessing that it's working, you can verify by having a look in your 
>> Galaxy server output/log file.  new_file_path will need to be set to 
>> something that is accessible on the cluster.
>> 
>> --nate
>> 
>>> 
>>> -Greg
>> 


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Re: [galaxy-user] Local Install - Understanding Upload File Concept

[Nate Coraor]

On Nov 16, 2012, at 10:41 AM, greg wrote:

> On Fri, Nov 16, 2012 at 10:00 AM, Nate Coraor  wrote:
>> On Nov 16, 2012, at 9:14 AM, greg wrote:
>> 
>> Are you running the upload tool on a cluster?
>> 
>> --nate
>> 
> 
> Well I have Galaxy set up to send it's jobs to SGE/qsub but I haven't
> verified that it's doing that yet.  I wanted to upload a file to test
> on first.
> 
> Here are the changes I made to universe_wsgi.ini after copying the sample:
> 
> 
>> #upload1 = local:///
> 

I'm guessing that it's working, you can verify by having a look in your Galaxy 
server output/log file.  new_file_path will need to be set to something that is 
accessible on the cluster.

--nate

> 
> -Greg


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Re: [galaxy-user] Local Install - Understanding Upload File Concept

[Nate Coraor]

On Nov 16, 2012, at 9:14 AM, greg wrote:

> I'm confused if files are uploaded through the Galaxy server or through 
> Apache?
> 
> I already set up the Apache proxy explained here:
> http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy
> (Does that affect uploads?)
> 
> My goal is to let users upload as large of files as possible through HTTP.

The file is uploaded "through" Apache, but Apache doesn't do anything special 
with it other than stream the bits through to Galaxy.  With nginx it's possible 
to have the proxy server actually handle the upload itself.

> So far I just tested and upload of a 140MB file and I got this error
> after a couple of minutes:
> 
> 1: dsim-all-chromosome-r1.3.fasta.msg.updated.fasta
> 0 bytes
> An error occurred running this job:Traceback (most recent call last):
> File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py",
> line 384, in 
> __main__()
> File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py",
> line 359, in __main__
> registry.load_datat
> 
> 
> I see this information in the bug report:
> 
> Traceback (most recent call last):
>  File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py",
> line 384, in 
>__main__()
>  File "/misc/local/galaxy/galaxy-dist/tools/data_source/upload.py",
> line 359, in __main__
>registry.load_datatypes( root_dir=sys.argv[1], config=sys.argv[2] )
>  File "/misc/local/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py",
> line 65, in load_datatypes
>tree = galaxy.util.parse_xml( config )
>  File "/misc/local/galaxy/galaxy-dist/lib/galaxy/util/__init__.py",
> line 143, in parse_xml
>tree = ElementTree.parse(fname)
>  File "build/bdist.linux-x86_64/egg/elementtree/ElementTree.py", line
> 859, in parse
>  File "build/bdist.linux-x86_64/egg/elementtree/ElementTree.py", line
> 576, in parse
> IOError: [Errno 2] No such file or directory: '/scratch/galaxy/tmptzuSYJ'
> Traceback (most recent call last):
>  File "./scripts/set_metadata.py", line 118, in 
>__main__()
>  File "./scripts/set_metadata.py", line 68, in __main__
>datatypes_registry.load_datatypes( root_dir=config_root,
> config=datatypes_config )
>  File "/misc/local/galaxy/galaxy-dist/lib/galaxy/datatypes/registry.py",
> line 65, in load_datatypes
>tree = galaxy.util.parse_xml( config )
>  File "/misc/local/galaxy/galaxy-dist/lib/galaxy/util/__init__.py",
> line 143, in parse_xml
>tree = ElementTree.parse(fname)
>  File "build/bdist.linux-x86_64/egg/elementtree/ElementTree.py", line
> 859, in parse
>  File "build/bdist.linux-x86_64/egg/elementtree/ElementTree.py", line
> 576, in parse
> IOError: [Errno 2] No such file or directory: '/scratch/galaxy/tmptzuSYJ'
> 
> 
> Also here is what /scratch/galaxy looks like.  It seems like the file
> it mentions does exist??
> 
>> ls -lh /scratch/galaxy/
> total 134M
> -rw-r--r-- 1 galaxy scicomp  20K Nov 13 13:35 tmpfCaiGX
> -rw-r--r-- 1 galaxy scicomp  20K Nov 14 13:36 tmpM2Wclq
> -rw-r--r-- 1 galaxy scicomp  20K Nov 14 13:35 tmpsIyPur
> -rw-r--r-- 1 galaxy scicomp  20K Nov 16 08:48 tmptY5RaM
> -rw-r--r-- 1 galaxy scicomp  20K Nov 16 08:54 tmptzuSYJ
> -rw-r--r-- 1 galaxy scicomp  20K Nov 15 15:47 tmpu77PEK
> -rw--- 1 galaxy scicomp  286 Nov 16 08:58 tmpykoBIq
> -rw--- 1 galaxy scicomp 134M Nov 16 08:58 upload_file_data_G3eZEg

Are you running the upload tool on a cluster?

--nate

> 
> Thanks,
> 
> Greg
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Re: [galaxy-user] [galaxy-dev] Account had be deleted ?

[Nate Coraor]

On Nov 7, 2012, at 5:47 AM, Diam Hsu wrote:

> Dear Sir or Madam,
> 
> 
> 
> I used to use Galaxy to analyze NGS data, but these two days I could't login 
> my Galaxy account, it also told me that my account has been marked deleted, 
> and asked me to contact the Galaxy administrator to restore my account.
> 
>  
> Could you help me restore my accounts because I have to use Galaxy to finish 
> my thesis.

Hi,

Your account was disabled because we discovered that you were using more than 
one account.  The Galaxy Main server is a public resource and we implemented 
quotas to give everyone fair access to our (limited) resources.  If you need 
more resources than we are able to make available on Galaxy Main, your needs 
might be best suited to a cloud or local instance of Galaxy. For more 
information on these, see:

  http://wiki.g2.bx.psu.edu/Big%20Picture/Choices

If you'd like to use one of your existing accounts, please let me know which 
one and I'll re-enable it.

--nate

> 
>  
> Thank you very much for your help!!!
> 
>  
> Best regards,
> 
>  
> Dima Hsu
> 
>  
> Graduate student,
> 
> Graduate Institute of Biomedical Informatics
> 
> Taipei Medical University, Taipei, Taiwan
> 
> Email:b1984...@gmail.com
> 
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> and other Galaxy lists, please use the interface at:
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Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg

[Nate Coraor]

On Nov 5, 2012, at 3:40 PM, greg wrote:

> Ok, that makes sense.
> 
> Would you mind sharing how you set up your init script?
> 
> What goes in it, where you place it?

There are some sample init scripts in the contrib/ directory of the 
distribution.  You should be able to place the export near the top, where other 
variables are set.

--nate

> 
> Thanks again,
> 
> Greg
> 
> On Mon, Nov 5, 2012 at 3:33 PM, Nate Coraor  wrote:
>> On Nov 5, 2012, at 3:26 PM, greg wrote:
>> 
>>> Well, I want it to ultimately run under Apache.  Does it still make
>>> sense to go in an init script?
>>> 
>>> thanks again,
>> 
>> Yes, even when running behind Apache, you'll need an init script (or similar 
>> method) to start the Galaxy server.
>> 
>> --nate
>> 
>>> 
>>> Greg
>>> 
>>> On Mon, Nov 5, 2012 at 3:23 PM, Nate Coraor  wrote:
>>>> On Nov 5, 2012, at 3:15 PM, greg wrote:
>>>> 
>>>>> And am I correct in the thinking that only the machine hosting the
>>>>> galaxy web interface and submitting jobs needs the export
>>>>> DRMAA_LIBRARY_PATH= variable?
>>>>> 
>>>>> The normal nodes running jobs don't need this, right?
>>>> 
>>>> Hi Greg,
>>>> 
>>>> That's correct.  If you're starting Galaxy with an init script, I'd put 
>>>> the export there.
>>>> 
>>>> --nate
>>>> 
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> -Greg
>>>>> 
>>>>> On Mon, Nov 5, 2012 at 3:12 PM, greg  wrote:
>>>>>> Thanks Scott.  I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0
>>>>>> 
>>>>>> I guess that would be it.
>>>>>> 
>>>>>> For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable
>>>>>> permanent on the machine?
>>>>>> 
>>>>>> -Greg
>>>>>> 
>>>>>> 
>>>>>> On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus 
>>>>>> wrote:
>>>>>>> 
>>>>>>> I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need
>>>>>>> DRMAA_LIBRARY_PATH to point to the library being used. So in the example
>>>>>>> below, I had this:
>>>>>>> 
>>>>>>>> echo $DRMAA_LIBRARY_PATH
>>>>>>> /usr/lib/libdrmaa.so
>>>>>>> 
>>>>>>> -Scott
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> Have you installed SGE on the same machine? If so, then you should be 
>>>>>>> able
>>>>>>> to
>>>>>>> do a "locate libdrmaa.so", which should point to SGE's DRMAA library. 
>>>>>>> For
>>>>>>> example,
>>>>>>> on a machine that I use, I see this:
>>>>>>> 
>>>>>>> $ locate libdrmaa.so
>>>>>>> /usr/lib/libdrmaa.so
>>>>>>> /usr/lib/libdrmaa.so.1.0
>>>>>>> $ ls /usr/lib/libdrmaa*
>>>>>>> /usr/lib/libdrmaa.so  /usr/lib/libdrmaa.so.1.0
>>>>>>> $ ls -la /usr/lib/libdrmaa.so
>>>>>>> lrwxrwxrwx 1 root root 15 Apr 18  2012 /usr/lib/libdrmaa.so ->
>>>>>>> libdrmaa.so.1.0
>>>>>>> 
>>>>>>> You may also want to try "updatedb" (again, assuming you're using Linux)
>>>>>>> to index
>>>>>>> the files on your machine. Finally, if you can't find it, then you 
>>>>>>> should
>>>>>>> check if you
>>>>>>> actually have SGE installed on that machine. I like to use "dpkg" on
>>>>>>> Ubuntu/Debian
>>>>>>> and "yum" on Centos to manipulate packages.
>>>>>>> 
>>>>>>> -Scott
>>>>>>> 
>>>>>>> 
>>>>>>> 
>>>>>>> I'm trying to install Galaxy on our SGE cluster (using the Unified
>>>>>>> method).
>>>>>>> 
>>>>>>> I installed galaxy-dist, and now I'm on this section:
>>>>>>

Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg

[Nate Coraor]

On Nov 5, 2012, at 3:26 PM, greg wrote:

> Well, I want it to ultimately run under Apache.  Does it still make
> sense to go in an init script?
> 
> thanks again,

Yes, even when running behind Apache, you'll need an init script (or similar 
method) to start the Galaxy server.

--nate

> 
> Greg
> 
> On Mon, Nov 5, 2012 at 3:23 PM, Nate Coraor  wrote:
>> On Nov 5, 2012, at 3:15 PM, greg wrote:
>> 
>>> And am I correct in the thinking that only the machine hosting the
>>> galaxy web interface and submitting jobs needs the export
>>> DRMAA_LIBRARY_PATH= variable?
>>> 
>>> The normal nodes running jobs don't need this, right?
>> 
>> Hi Greg,
>> 
>> That's correct.  If you're starting Galaxy with an init script, I'd put the 
>> export there.
>> 
>> --nate
>> 
>>> 
>>> Thanks,
>>> 
>>> -Greg
>>> 
>>> On Mon, Nov 5, 2012 at 3:12 PM, greg  wrote:
>>>> Thanks Scott.  I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0
>>>> 
>>>> I guess that would be it.
>>>> 
>>>> For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable
>>>> permanent on the machine?
>>>> 
>>>> -Greg
>>>> 
>>>> 
>>>> On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus 
>>>> wrote:
>>>>> 
>>>>> I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need
>>>>> DRMAA_LIBRARY_PATH to point to the library being used. So in the example
>>>>> below, I had this:
>>>>> 
>>>>>> echo $DRMAA_LIBRARY_PATH
>>>>> /usr/lib/libdrmaa.so
>>>>> 
>>>>> -Scott
>>>>> 
>>>>> 
>>>>> 
>>>>> Have you installed SGE on the same machine? If so, then you should be able
>>>>> to
>>>>> do a "locate libdrmaa.so", which should point to SGE's DRMAA library. For
>>>>> example,
>>>>> on a machine that I use, I see this:
>>>>> 
>>>>> $ locate libdrmaa.so
>>>>> /usr/lib/libdrmaa.so
>>>>> /usr/lib/libdrmaa.so.1.0
>>>>> $ ls /usr/lib/libdrmaa*
>>>>> /usr/lib/libdrmaa.so  /usr/lib/libdrmaa.so.1.0
>>>>> $ ls -la /usr/lib/libdrmaa.so
>>>>> lrwxrwxrwx 1 root root 15 Apr 18  2012 /usr/lib/libdrmaa.so ->
>>>>> libdrmaa.so.1.0
>>>>> 
>>>>> You may also want to try "updatedb" (again, assuming you're using Linux)
>>>>> to index
>>>>> the files on your machine. Finally, if you can't find it, then you should
>>>>> check if you
>>>>> actually have SGE installed on that machine. I like to use "dpkg" on
>>>>> Ubuntu/Debian
>>>>> and "yum" on Centos to manipulate packages.
>>>>> 
>>>>> -Scott
>>>>> 
>>>>> 
>>>>> 
>>>>> I'm trying to install Galaxy on our SGE cluster (using the Unified
>>>>> method).
>>>>> 
>>>>> I installed galaxy-dist, and now I'm on this section:
>>>>> 
>>>>> drmaa egg
>>>>> 
>>>>> The drmaa egg is provided by Galaxy, but you must tell it where your
>>>>> resource manager's DRMAA library is located, and this is done with
>>>>> the$DRMAA_LIBRARY_PATH environment variable:
>>>>> 
>>>>> % export
>>>>> DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3
>>>>> % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0
>>>>> 
>>>>> 
>>>>> However I can't locate the the file libdrmaa.so.1.0.3 anywhere.  In fact I
>>>>> don't have have an lsf nor sge directory within galaxy-dist.
>>>>> 
>>>>> Thanks,
>>>>> 
>>>>> Greg
>>>>> 
>>>>> ___
>>>>> 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 discussio

Re: [galaxy-user] Cluster Install - Trouble finding drmaa egg

[Nate Coraor]

On Nov 5, 2012, at 3:15 PM, greg wrote:

> And am I correct in the thinking that only the machine hosting the
> galaxy web interface and submitting jobs needs the export
> DRMAA_LIBRARY_PATH= variable?
> 
> The normal nodes running jobs don't need this, right?

Hi Greg,

That's correct.  If you're starting Galaxy with an init script, I'd put the 
export there.

--nate

> 
> Thanks,
> 
> -Greg
> 
> On Mon, Nov 5, 2012 at 3:12 PM, greg  wrote:
>> Thanks Scott.  I did turn up: /sge/8.0.1p4/lib/lx-amd64/libdrmaa.so.1.0
>> 
>> I guess that would be it.
>> 
>> For a followup question ,how do I make the DRMAA_LIBRARY_PATH variable
>> permanent on the machine?
>> 
>> -Greg
>> 
>> 
>> On Mon, Nov 5, 2012 at 3:03 PM, Scott McManus 
>> wrote:
>>> 
>>> I forgot to add my value of DRMAA_LIBRARY_PATH. Note that I just need
>>> DRMAA_LIBRARY_PATH to point to the library being used. So in the example
>>> below, I had this:
>>> 
 echo $DRMAA_LIBRARY_PATH
>>> /usr/lib/libdrmaa.so
>>> 
>>> -Scott
>>> 
>>> 
>>> 
>>> Have you installed SGE on the same machine? If so, then you should be able
>>> to
>>> do a "locate libdrmaa.so", which should point to SGE's DRMAA library. For
>>> example,
>>> on a machine that I use, I see this:
>>> 
>>> $ locate libdrmaa.so
>>> /usr/lib/libdrmaa.so
>>> /usr/lib/libdrmaa.so.1.0
>>> $ ls /usr/lib/libdrmaa*
>>> /usr/lib/libdrmaa.so  /usr/lib/libdrmaa.so.1.0
>>> $ ls -la /usr/lib/libdrmaa.so
>>> lrwxrwxrwx 1 root root 15 Apr 18  2012 /usr/lib/libdrmaa.so ->
>>> libdrmaa.so.1.0
>>> 
>>> You may also want to try "updatedb" (again, assuming you're using Linux)
>>> to index
>>> the files on your machine. Finally, if you can't find it, then you should
>>> check if you
>>> actually have SGE installed on that machine. I like to use "dpkg" on
>>> Ubuntu/Debian
>>> and "yum" on Centos to manipulate packages.
>>> 
>>> -Scott
>>> 
>>> 
>>> 
>>> I'm trying to install Galaxy on our SGE cluster (using the Unified
>>> method).
>>> 
>>> I installed galaxy-dist, and now I'm on this section:
>>> 
>>> drmaa egg
>>> 
>>> The drmaa egg is provided by Galaxy, but you must tell it where your
>>> resource manager's DRMAA library is located, and this is done with
>>> the$DRMAA_LIBRARY_PATH environment variable:
>>> 
>>> % export
>>> DRMAA_LIBRARY_PATH=/galaxy/lsf/7.0/linux2.6-glibc2.3-x86_64/lib/libdrmaa.so.1.0.3
>>> % export DRMAA_LIBRARY_PATH=/galaxy/sge/lib/lx24-amd64/libdrmaa.so.1.0
>>> 
>>> 
>>> However I can't locate the the file libdrmaa.so.1.0.3 anywhere.  In fact I
>>> don't have have an lsf nor sge directory within galaxy-dist.
>>> 
>>> Thanks,
>>> 
>>> Greg
>>> 
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Re: [galaxy-user] Import files from filesystem path : No redundance?

[Nate Coraor]

On Oct 26, 2012, at 10:32 AM, julie dubois wrote:

> Hi all,
> I have used the option "Import files from filesystem path" to import a 
> complete arborescence of directories and files in one Data Library of Galaxy.
> 
> Lot of files and sub-directories wil add to this arborescence.
> I've hoped import those changes in my data library with the option : add 
> datasets, then indicate the path of this arborescence at the option "import 
> from filesystem path".
> But when I use this way, Galaxy re-import all arborescence : the new files 
> and sub-directories AND all already imported directories and files!
> 
> Is there a way to import just the new files without know a priori which are 
> new in my arborescence? 
> Thanks.

Hi Julie,

This function is designed for single-time imports.  To maintain synchronization 
between your filesystem and Galaxy, I'd suggest writing an API script.

--nate

> 
> Julie
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Re: [galaxy-user] Can't seem to stop or restart the Galaxy in server

[Nate Coraor]

On Oct 18, 2012, at 1:43 AM, Todd Oakley wrote:

> Yes, daemon/stop-daemon is the best way.  However, to stop a process that was 
> not started with --daemon, this is what I do:
> 
>  ps aux | grep galaxy
> 
> Identify the process numbers for 3 Galaxy processes, which will change every 
> time Galaxy is restarted.
> For example this line:
>  galaxy   11638  0.0  0.0  63856   988 ?SNov10   0:00 /bin/sh 
> ./run.sh --reload
> 
> indicates the process has a number of 11638.
> The 3 processes look like:
>   • /bin/sh ./run.sh --reload
>   • python ./scripts/paster.py serve universe_wsgi.ini --reload
>   • /home/galaxy/bin/python ./scripts/paster.py serve universe_wsgi.ini 
> --reload
> Next, kill the three processes with this command:
>  kill -9   

Hi Todd,

Are you unable to Ctrl+C when using --reload?  Using --reload is actually my 
workaround for this problem.

--nate

> 
> 
> 
> 
> 
> On Oct 17, 2012, at 10:17 PM, Enis Afgan wrote:
> 
>> With a certain version of Python there's been an issue stopping Galaxy using 
>> ctrl+C. You can use 'sh run.sh --daemon' to have the process run in the 
>> background and then 'sh run.sh --stop-damemon' to stop it.
>> 
>> Hope this helps,
>> Enis
>> 
>> On Thu, Oct 18, 2012 at 4:12 PM, Sachit Adhikari 
>>  wrote:
>> Hello Everyone. Ctrl+C or Ctrl+D doesn't stop the Galaxy server. In local 
>> machine, I need to close the terminal and restart the terminal again. 
>> However, in server I integrated several tools, now I need to restart the 
>> server to test it. I used ./run.sh --reload doesn't restart the server and I 
>> can't stop the server. How can I stop or restart Galaxy in the real working 
>> server? Thanks 
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Re: [galaxy-user] Fastq-groomer help

[Nate Coraor]

On Oct 3, 2012, at 2:02 PM, Kshama Aswath wrote:

> Hello:
> I have this 20GB data that I have uploaded onto my history and trying to get 
> it run thr groomer. Just the first data set was uploaded yesterday and ran 
> groomer on it and it was not done this morning. The message indicated taht it 
> is still waiting to be run !!! I have 57 data sets to run and would 
> appreciate if you could inform me about how long it may take to even get 
> started or any other suggestion to get my job done will help.
> Thanks so much, user name :genenart
> Kshama.

Hi Kshama,

There were some problems dispatching jobs that have been resolved.  Sorry for 
the inconvenience, and thanks for using Galaxy.

--nate

> 
> -- 
> Kshama Aswath
> Graduate Student-(PhD)
> Bioinformatics and computational Biology
> Prince Williams Campus
> George Mason University
> Manasses,VA-20110
> 
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Re: [galaxy-user] Installing Galaxy on SGE Cluster - Questions

[Nate Coraor]

On Oct 2, 2012, at 3:26 PM, greg wrote:

> On Tue, Oct 2, 2012 at 2:15 PM, Nate Coraor  wrote:
>> Hi Greg,
>> 
>> You should start at the top level documentation for production servers:
>> 
>>http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server
>> 
>> This includes instructions on how to set up a virtualenv.  You can make this 
>> the default by setting the $PATH in the Galaxy user's ~/.bash_profile to 
>> include the virtualenv's bin directory (at the beginning of $PATH).
> 
> This makes sense, but I ultimately want to run the jobs as the logged
> in user as per this page:
> http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster#Submitting_Jobs_as_the_Real_User
> 
> It wouldn't be feasible to add the virtualenv to every users' path.
> I'm hoping there's some kind of other way?

Indeed there is.  Have a look at the 'environment_setup_file' option in the 
config file.

--nate

> 
> Thanks again,
> 
> Greg


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Re: [galaxy-user] Installing Galaxy on SGE Cluster - Questions

[Nate Coraor]

On Oct 2, 2012, at 12:45 PM, greg wrote:

> Hi guys,
> 
> I'm following the instructions here to install Galaxy on our SGE cluster.
> http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster
> (I'm aiming for the unified install)
> 
> Here are a couple of questions I'm hoping someone could clear up for me:
> 
> How exactly do I use virtual env to make Galaxy install all the Python
> libraries there instead of on the system?  How will Galaxy know to use
> the virtualenv to run and to use it for grid jobs?

Hi Greg,

You should start at the top level documentation for production servers:

http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server

This includes instructions on how to set up a virtualenv.  You can make this 
the default by setting the $PATH in the Galaxy user's ~/.bash_profile to 
include the virtualenv's bin directory (at the beginning of $PATH).

> Do I need to install all of the dependencies listed on this page:
> http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies
> If so what's a good way to make sure they're contained in the
> galaxy-dist directory and make sure Galaxy and all of the jobs know to
> find these tools there?

You only need to install the dependencies for the tools that you plan to use.  
Setting them up is explained in more detail here:

http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies

--nate

> 
> Thanks,
> 
> Greg
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Re: [galaxy-user] interupted running jobs restart

[Nate Coraor]

On Aug 27, 2012, at 8:53 AM, petr wrote:

> We are running galaxy on pbs cluster. In out setting some jobs can take
> several weeks to finish and it is virtually impossible to wait for suitable
> moment when server can be restarted or turn down without interrupting
> running tasks. Is there an option on server setting which will enable jobs
> which were interrupted because of the server maintenance to run again after
> the cluster is back on?
> best regards.
> Petr

Hi Petr,

Galaxy automatically picks up jobs that were running via PBS when it's 
restarted.  Only local jobs can't be recovered after a restart.  Is this not 
working properly in your environment?

--nate

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Re: [galaxy-user] file upload renamed

[Nate Coraor]

Hi Neil,

You're looking for the option to "link to" data, which is explained here:

http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files

--nate

On Aug 22, 2012, at 12:44 AM,  wrote:

> When uploading a file using “Get Data” it seems the file is renamed to 
> dataset_’id’.dat in ~/database/files/000/. Is it possible for the file to 
> keep its name rather than being renamed?
> 
> It seems this is being done because of the line 
> 
> ${output.dataset.dataset.id}:${output.files_path}:${file_name}
> 
> in the upload.xml file. But I don't know where in the code it gets 
> ${file_name} from. Any ideas how i change this to get the correct name of the 
> file being uploaded?
> 
> Neil
> 
> 
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Re: [galaxy-user] Job is waiting to run for two days..

[Nate Coraor]

On Jun 25, 2012, at 1:53 PM, Shanshan Pang wrote:

> Hi, I am in the step "map with bowtie" with a status of JOB IS WAITING TO RUN 
> for two days. I tried to re-run it, but did not work. So any suggestions on 
> it?
> Thanks!

Hi Shanshan,

The cluster used to run mapping and other NGS tools is very busy right now.  
Canceling and rerunning your job moves it to the bottom of the queue, so I 
would not suggest doing that.

If your work is urgent, a cloud instance is the recommended alternative for 
large NGS jobs:

http://getgalaxy.org/cloud

--nate

> 
> Shanshan
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Re: [galaxy-user] Include a data folder into Galaxy

[Nate Coraor]

On Jun 25, 2012, at 2:49 AM, Björn Grüning wrote:

> Hi Norbert,
> 
> please have a look at the FTP-Upload feature from galaxy.
> The idea is that every user gets an FTP folder in which he can upload
> data. If you create such a directory you can probably link your data in
> such directories and galaxy will offer them to the users in the upload
> tool.

In addition to FTP uploads for users, you may find the Data Library upload 
options useful:

http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files

--nate

> 
> Hope that helps.
> Cheers,
> Bjoern
> 
>> Hello,
>> 
>> hopefully this is a simple question: How can I include a folder into the 
>> Galaxy server?
>> 
>> The backgroud is, that I installed Galaxy on one of out server, which 
>> has access to the data folders used everywhere at our institute.  So, 
>> instead of uploading and copying serveral big files (and waisting space 
>> on servers) I want to make a link to the appropiate folder, so it can be 
>> used like as the data has been uploaded.  I hope I explained enough 
>> details...  The question is: is it possible?
>> 
>> Thanks for help, Norbert
>> 
> 
> 
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Re: [galaxy-user] jobs not running on main server

[Nate Coraor]

On Jun 16, 2012, at 7:31 PM, Jacob Musser wrote:

> Hello,
> 
> I uploaded a couple small files via ftp to do some basic text manipulation on 
> them in the main galaxy server.  I have queued up several jobs (including 
> just importing the files I uploaded into a history) but after two hours of 
> waiting they are still gray and "waiting to run."   I have been using galaxy 
> regularly lately and have never had to wait very long for a job to start 
> running (usually a matter of seconds).  I am not above my quota so this is 
> not the problem.  Is there something else I need to do or is there a problem 
> with the servers that would explain why jobs aren't being run?

Hi Jake,

There was a problem with our cluster scheduler that was resolved on Saturday 
night.  Please let us know if you still have problems running jobs.

--nate

> 
> All the best,
> Jake
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Re: [galaxy-user] Galaxy main not running jobs..

[Nate Coraor]

On Jun 16, 2012, at 7:38 PM, Jayaraman, Shyam wrote:

> Hi,
> 
> My username is shyamsundar19...@gmail.com
> 
> Galaxy main is not running jobs since today morning. They stay queued (gray) 
> forever. I deleted and then re queued them twice. Still nothing.. Is the 
> server down or is something wrong with my account??

Hi Shyam,

There was a problem with our cluster scheduler that was resolved on Saturday 
night.  Please let us know if you still have problems running jobs.

--nate

> 
> Kindly advice.
> 
> 
> Shyam S Jayaraman MD
> Staff Research Associate
> Division of Dermatology
> LABioMed Research Institute
> CA
> 
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Re: [galaxy-user] FTP down?

[Nate Coraor]

On Jun 14, 2012, at 12:17 PM, John Clayton wrote:

> Dear Sir or Madam,
> 
> I have been attempting to upload a few datasets (>2Gb) for the past few days 
> but I cannot seem to login to the server. This has been the case since the 
> server crashed last week. Could you please restart the ftp server?

Hi John,

>From the logs, it appears you're using your Galaxy username rather than your 
>full email address to log in.  Please try with your email address, and let us 
>know if it works.

--nate

> 
> Many thanks,
> 
> John
> 
> -- 
> John R. Clayton, PhD
> Université de Strasbourg
> Anopheles Group, CNRS UPR-9022
> "Réponse Immunitaire et Développement chez les Insectes"
> Institut de Biologie Moléculaire et Cellulaire (IBMC)
> 15, rue René Descartes F-67084 CEDEX Strasbourg France
> 
> Tel: +33 3.88.41.70.96
> Fax: +33 3.88.60.69.22
> 
> Email: j.clay...@ibmc-cnrs.unistra.fr
> 
> http://www-ibmc.u-strasbg.fr/ridi/index.php?cont_id=9&lang=en
> 
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Re: [galaxy-user] Problem using Galaxy

[Nate Coraor]

Hi,

Please try starting with:

$ LC_ALL=C ./run.sh

--nate

On May 18, 2012, at 11:22 AM, Seyed Mehdi Jazayeri wrote:

> 
> Dear Sir/Madam,
> 
> I am a PhD student working on RNA-Seq as my dissertation. As a matter of fact 
> I want to do analyses of gene expressions for the sequences that I have and 
> for that I have tried to use Galaxy tools as it is one of the best platforms 
> in order to do analysis for RNA-Seq as well as others. I did all about 
> installation of Galaxy on my Mac OS 10.7 Lion but when I run the commands I 
> do not get any result from running any type of commands. And when I do run.sh 
> I will have nothing done. As a sample I send you the command I ran on my 
> system as follow
> 
> iMac-de-Biologia:galaxy-dist LabBioMol$ ./run.sh
> Traceback (most recent call last):
>   File "./scripts/paster.py", line 34, in 
> command.run()
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
>  line 84, in run
> invoke(command, command_name, options, args[1:])
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
>  line 123, in invoke
> exit_code = runner.run(args)
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/command.py",
>  line 218, in run
> result = self.command()
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py",
>  line 276, in command
> relative_to=base, global_conf=vars)
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteScript-1.7.3-py2.7.egg/paste/script/serve.py",
>  line 313, in loadapp
> **kw)
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
>  line 204, in loadapp
> return loadobj(APP, uri, name=name, **kw)
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
>  line 224, in loadobj
> global_conf=global_conf)
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
>  line 248, in loadcontext
> global_conf=global_conf)
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
>  line 278, in _loadconfig
> return loader.get_context(object_type, name, global_conf)
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
>  line 413, in get_context
> section)
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
>  line 458, in _context_from_explicit
> value = import_string(found_expr)
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/PasteDeploy-1.3.3-py2.7.egg/paste/deploy/loadwsgi.py",
>  line 18, in import_string
> return pkg_resources.EntryPoint.parse("x="+s).load(False)
>   File "/Users/LabBioMol/galaxy-python/galaxy-dist/lib/pkg_resources.py", 
> line 1954, in load
> entry = __import__(self.module_name, globals(),globals(), ['__name__'])
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/lib/galaxy/web/__init__.py", line 
> 5, in 
> from framework import expose, json, json_pretty, require_login, 
> require_admin, url_for, error, form, FormBuilder, expose_api
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/lib/galaxy/web/framework/__init__.py",
>  line 31, in 
> from babel.support import Translations
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg/babel/support.py",
>  line 29, in 
> from babel.dates import format_date, format_datetime, format_time, LC_TIME
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg/babel/dates.py",
>  line 34, in 
> LC_TIME = default_locale('LC_TIME')
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg/babel/core.py",
>  line 642, in default_locale
> return '_'.join(filter(None, parse_locale(locale)))
>   File 
> "/Users/LabBioMol/galaxy-python/galaxy-dist/eggs/Babel-0.9.4-py2.7.egg/babel/core.py",
>  line 763, in parse_locale
> raise ValueError('expected only letters, got %r' % lang)
> ValueError: expected only letters, got 'utf-8'
> iMac-de-Biologia:galaxy-dist LabBioMol$ 
> 
> 
> Now I would appreciate if you could advise me what is the problem and how to 
> solve it.
> 
> Thanks for your attention in advance.
> 
> Best regards
> 
> SMJ
> -- 
> SMJ
> 
> Seyed Mehdi Jazayeri
> 
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Re: [galaxy-user] "Job is waiting to run"

[Nate Coraor]

Hi Shisheng and Mónica,

I see that jobs weren't dispatching on Galaxy Main, and have gotten them moving 
again.  It'll take a bit to run through the backlog.  Sorry for the 
inconvenience, and thanks for using Galaxy.

--nate

On Mar 22, 2012, at 5:30 AM, Mónica Pérez Alegre wrote:

> Hi Shisheng
> 
> My partner and me have the same problem since yesterday.
> 
> We would be very grateful for any help.
> 
> regards
> 
> -Mensaje original-
> De: galaxy-user-boun...@lists.bx.psu.edu 
> [mailto:galaxy-user-boun...@lists.bx.psu.edu] En nombre de Shisheng Li
> Enviado el: miércoles, 21 de marzo de 2012 20:30
> Para: galaxy-user@lists.bx.psu.edu
> Asunto: [galaxy-user] "Job is waiting to run"
> 
> Dear Sir/Madam,
> 
> I am a registered user of the public Galaxy Server (main). Any job I
> submitted today is labeled as "Job is waiting to run" forever. The total
> volume of my files is 249 mb, which is far below the quota limit of 250 gb,
> and I am trying to run less than 8 jobs. Could you please let me know the
> possible reasons?
> 
> Sincerely,
> 
> Shisheng
> 
> 
> 
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Re: [galaxy-user] ftp

[Nate Coraor]

On Mar 20, 2012, at 8:13 AM, Richard Mark White wrote:

> Hi,
> Is anyone else having trouble connecting to main.g2.bx.psu.edu for FTP 
> uploads?  I cannot seem to connect since yesterday.

Hi Rich,

It's back up now.

--nate

> 
> Rich
> 
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Re: [galaxy-user] Error during data upload of fastq.gz

[Nate Coraor]

On Jan 31, 2012, at 3:46 AM, Stefan Kroeger wrote:

> 2012/1/30 Nate Coraor 
> Could you upload it to the FTP site and then send us the filename, without 
> attempting to import it using the "Upload File" tool in the web interface?  
> I'll grab a copy and take a look at it.
> 
> 
> unfortunately not, I'm not allowed to.
> but thanks for your help.

Is this in a local instance, then?  You'll have to take a look at 
tools/data_source/upload.py and have a look at the html checks to see where and 
why it's failing.  Have you checked the first and last lines of the file?  
That's occasionally the problem.

--nate

> 
> best 
> Stefan 
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Re: [galaxy-user] Error during data upload of fastq.gz

[Nate Coraor]

On Jan 30, 2012, at 11:37 AM, Stefan Kroeger wrote:

> Hi Jen,
> 
> On 30.01.2012 16:12, Jennifer Jackson wrote:
>> Are you still having this problem? One thought is that this file is some
>> sort of README file in with the other data files from you source.
>> Another is that the data is an annotation file, not a sequence file,
>> with one or more columns of data in HTML format.
> 
> yes I still have the problem, but to ensure it's not a file error I will
> check the original data from the lab.
> 
> if the problem is still present I will come back to you.
> 
>> Some things to check:
>> - have you opened/uncompressed the file locally to see if it contains
>> any HTML?
> 
> it's a complete lane so really hard to check by eye ;-)
> do you know any kind of "command line fasta validation tool"?
> 
>> - are you able to download, uncompress, and then load the file
>> uncompressed or does that also give errors? Using "upload from the
>> desktop" or "FTP"?
> 
> tried both, no changes.

Hi Stefan,

Could you upload it to the FTP site and then send us the filename, without 
attempting to import it using the "Upload File" tool in the web interface?  
I'll grab a copy and take a look at it.

--nate

> 
> Thanks & best regards
> Stefan
> 
>> [...]
>> 
>> On 1/26/12 5:55 AM, Stefan Kroeger wrote:
>>> hi,
>>> Maybe anybody can give me a hint for the following problem...
>>> 
>>> When I try to upload a fastq.gz file into galxy using url function the
>>> input os canceled with the following exception:
>>> 
>>> An error occurred running this job: The uploaded file contains
>>> inappropriate HTML content
>>> 
>>> I don't know where to start to have a look at. The upload of all other
>>> fastq.gz files from the same run works smooth.
>>> 
>>> best
>>>  stefan
>>> 
>>> PS. Yes I know, the problem is really unspecific, sorry for that...
>>> ___
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>> 
> 
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Re: [galaxy-user] ftp upload

[Nate Coraor]

On Dec 27, 2011, at 8:52 PM, Gabor Bartha wrote:

> I have tried to use ftp to upload files to main.g2.bx.psu.edu but the jobs 
> have been failing with:
> 421 service not available, remote server has closed connection
> after about 1.5GB.
>  
> Isn’t ftp the way you are supposed to upload large files?  The file I am 
> uploading is ~6GB in size. 

Hi Gabor,

You can resume the upload if it's interrupted.  I'll have a look at the logs to 
see if there is any indication why it's failed.

--nate

>  
> Gábor Bartha, Ph.D.
> Director of Information Sciences
> Synergenics, LLC
> 863 Mitten Rd., Suite 101
> Burlingame, CA 94010
> 650-777-5202
>  
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Re: [galaxy-user] problem upload data file

[Nate Coraor]

On Dec 28, 2011, at 10:36 AM, Eric Guo wrote:

> Hi everyone, 
> 
> I'd like to upload my sequencing data file, 36 GB, onto galaxy. My data is on 
> a computer cluster in my institute. So I use ssh shell ftp commands to 
> connect to galaxy and upload the data(ftp> put filename). And the connection 
> appears to be fine as far as I can tell.
> 
> I tried few times. Every time the uploading is fine in the beginning. 
> However, when about 12 GB of my dataset is uploaded (according to Galaxy 
> upload file page), the upload stops, and an error message pop up in the 
> terminal on my Mac saying "a broken pipeline". 
> 
> I never had this problem before when I was using FTP programs like CyberDuck. 
> Has anyone have similar problems using ssh command lines to upload data? 
> What's the correct way to upload data from a computer cluster?
> 
> Thanks in advance for your help. 

Hi Eric,

I'm not sure what's causing the connection to die, but I'd suggest using rsync 
so at least it can be resumed.

--nate

> 
> -Eric
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Re: [galaxy-user] Not able to get data from UCSC table browser

[Nate Coraor]

On Dec 22, 2011, at 5:35 PM, Sell, Christian wrote:

> Hi,
>  
> I encountered similar problems today. I can’t open some histories, upload 
> data or transfer data between histories.
>  
> Regards
>  
> Christian

Hi,

Due to extremely high load at the time, jobs were delayed.  This has been 
resolved, so please let us know if you have any further problems with running 
jobs.  Sorry for the inconvenience and thanks for using Galaxy.

Thanks,
--nate

>  
>  
> Von: galaxy-user-boun...@lists.bx.psu.edu 
> [mailto:galaxy-user-boun...@lists.bx.psu.edu] Im Auftrag von Mike Dufault
> Gesendet: Donnerstag, 22. Dezember 2011 23:02
> An: galaxy-user@lists.bx.psu.edu
> Betreff: Re: [galaxy-user] Not able to get data from UCSC table browser
>  
> Hi Galaxy team,
>  
> I also am having a similar problem. I uploaded data by ftp but when I try to 
> load into a work history, it is stuck as  "Job waiting to run."
>  
> Mike
> 
> 
> 
> --- On Thu, 12/22/11, Peng Yu  wrote:
> 
> From: Peng Yu 
> Subject: [galaxy-user] Not able to get data from UCSC table browser
> To: galaxy-user@lists.bx.psu.edu
> Date: Thursday, December 22, 2011, 12:06 AM
> 
> Hi,
> 
> I'm trying to get data from UCSC table browser. However, the browser
> always show "Waiting for main.g2.bx.psu.edu...". Is there any problem
> with the galaxy server?
> 
> -- 
> Regards,
> Peng
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Re: [galaxy-user] Tophat jobs not starting

[Nate Coraor]

On Dec 14, 2011, at 11:19 AM, Magdalena Strzelecka wrote:

> Hi, 
> 
> I have submitted some jobs to Tophat, but they have not started since 
> yesterday (Dec 13th); i.e they were in a queue for >12 hrs. I have 
> re-submitted everything again (2 jobs), but the same situation is happening. 
> Is there some issue with Tophat at the moment?

Hi Magdalena,

This was due to a problem with the cluster Galaxy uses to run certain jobs. 
This was resolved early last week, although there may have been a few 
intermittent problems after that time. If tophat still has not run 
successfully, please let us know.

Our sincere apologies for the inconvenience,

Best,
--nate

> Thanks.
> M.
> 
> --
> Magdalena Strzelecka, PhD
> 
> Heald Lab
> University of California, Berkeley
> Department of Molecular & Cell Biology
> 315 Life Sciences Addition # 3200
> Berkeley, CA 94720-3200
> 
> phone: (510) 643-5002
> fax: (510) 643-6791
> e-mail: strzele...@berkeley.edu
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
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Re: [galaxy-user] Finding Galaxy version

[Nate Coraor]

On Dec 13, 2011, at 5:33 AM, Paul-Michael Agapow wrote:

> A perhaps obvious question: how do I work out what version of Galaxy an 
> instance is?
>  
> This has come  up a few times because of apparent bugs and different 
> behaviour across various development and production instances. Now if you’re 
> installed straight from the repo, you can use “hg log” for the repo number. 
> But that doesn’t work if it’s been installed in another way, say from a 
> tarball or via another versioning system (we use git to synchronize tool 
> development to a production server).
>  
> Simple solution?

Hi Paul,

Since the hg changeset id is the Galaxy version, there's not a great way to 
determine the version without hg.  I'd suggest making a note of the id when you 
fetch the tarball.

--nate

>  
> 
> Paul Agapow (paul-michael.aga...@hpa.org.uk)
> Bioinformatics, Health Protection Agency
>  
> 
> 
> ** 
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Re: [galaxy-user] is public galaxy down?

[Nate Coraor]

On Dec 17, 2011, at 8:34 AM, Richard Mark White wrote:

> I am unable to access for past several hours.  Are others having the same 
> issue?

Hi Rich,

Our core router has crashed, we're working on the problem and hope to have it 
fixed within the next few hours.  Sorry for the inconvenience.

--nate

> 
> rich
> 
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Re: [galaxy-user] disk quota not updating

[Nate Coraor]

On Nov 30, 2011, at 12:49 PM, Richard Mark White wrote:

> Hi,
>   I was nearing my disk quota (at 97%), so I deleted a large number of 
> datasets using "delete permanently".  But my usage did not go down at all.  
> Is there a delay in this happening, or is there some way to purge the files?

Hi Richard,

It can take a bit if you delete a large amount of data at once.  Did your usage 
eventually decrease?

--nate

> 
> richard
> 
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Re: [galaxy-user] Lastz

[Nate Coraor]

On Nov 12, 2011, at 6:30 AM, Andrew South wrote:

> Dear Nate -
>  
>  It seems I may have upset the cluster again: I have 3 Lastz jobs running and 
> cannot upload any more data. I had been uploading fine; started 3 lastz 
> mapping jobs (Fasta (1 sequence) vs Fasta (~3000 sequences) output as SNP, 
> when I realised I made a mistake, cancelled these jobs, uploaded the correct 
> files and then ran the 3 comparisons (similar files) again and now these jobs 
> have been running >1hr and I cannot upload any more data.

Hi Andy,

What are the details related to being unable to upload?  Are the datasets 
sitting in a certain state (uploading, queued, etc.)?  Did you have any other 
jobs running at the time?  There are some concurrent job limits that could have 
been responsible.

--nate

>  
> Thanks in advance,
> 
> Andy
>  
> 
> Please consider the environment. Do you really need to print this email?
> 
> 
> >>> Nate Coraor  11/11/2011 17:16 >>>
> On Nov 11, 2011, at 10:01 AM, Andrew South wrote:
> 
> > Thanks Nate, hope it's a quick fix. Best wishes, Andy
> 
> Hi Andy,
> 
> All backlogged NGS jobs should now be running, new ones will likely queue 
> until free slots are available.  Please let us know if there's further 
> trouble, and thanks for using Galaxy,
> 
> --nate
> 
> >  
> > ****
> > Please consider the environment. Do you really need to print this email?
> > 
> > 
> > >>> Nate Coraor  11/11/2011 14:55 >>>
> > On Nov 11, 2011, at 9:21 AM, Andrew South wrote:
> > 
> > > Hello folks
> > >  
> > >  Anyone else having trouble with running Lastz to map?
> > >  
> > >  Jobs are being sent but not running.
> > >  
> > >  It stopped working for me two days ago after working perfectly, I've 
> > > tried fiddling with the formats but no joy.
> > 
> > Hi Andy,
> > 
> > It looks like there's a problem with the cluster that runs our NGS jobs.  
> > I'm currently looking into it.  Sorry for the inconvenience.
> > 
> > --nate
> > 
> > >  
> > > Thanks,
> > > 
> > > Andy
> > >  
> > >  
> > > Dr A P South 
> > > Centre for Oncology and Molecular Medicine
> > > University of Dundee
> > > Ninewells Hospital & Medical School
> > > Dundee
> > > DD1 9SY
> > > Tel 01382 496432
> > > Fax 01382 633952
> > >  
> > > a.p.so...@dundee.ac.uk
> > >  
> > >  
> > > 
> > > Please consider the environment. Do you really need to print this email?
> > > 
> > > The University of Dundee is a registered Scottish charity, No: SC015096
> > > 
> > > ___
> > > The Galaxy User list should be used for the discussion of
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> > > 
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> > > 
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> > > please use the interface at:
> > > 
> > >  http://lists.bx.psu.edu/
> > 
> > 
> > The University of Dundee is a registered Scottish charity, No: SC015096
> > 
> 
> 
> The University of Dundee is a registered Scottish charity, No: SC015096
> 


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Re: [galaxy-user] Lastz

[Nate Coraor]

On Nov 11, 2011, at 10:01 AM, Andrew South wrote:

> Thanks Nate, hope it's a quick fix. Best wishes, Andy

Hi Andy,

All backlogged NGS jobs should now be running, new ones will likely queue until 
free slots are available.  Please let us know if there's further trouble, and 
thanks for using Galaxy,

--nate

>  
> 
> Please consider the environment. Do you really need to print this email?
> 
> 
> >>> Nate Coraor  11/11/2011 14:55 >>>
> On Nov 11, 2011, at 9:21 AM, Andrew South wrote:
> 
> > Hello folks
> >  
> >  Anyone else having trouble with running Lastz to map?
> >  
> >  Jobs are being sent but not running.
> >  
> >  It stopped working for me two days ago after working perfectly, I've tried 
> > fiddling with the formats but no joy.
> 
> Hi Andy,
> 
> It looks like there's a problem with the cluster that runs our NGS jobs.  I'm 
> currently looking into it.  Sorry for the inconvenience.
> 
> --nate
> 
> >  
> > Thanks,
> > 
> > Andy
> >  
> >  
> > Dr A P South 
> > Centre for Oncology and Molecular Medicine
> > University of Dundee
> > Ninewells Hospital & Medical School
> > Dundee
> > DD1 9SY
> > Tel 01382 496432
> > Fax 01382 633952
> >  
> > a.p.so...@dundee.ac.uk
> >  
> >  
> > 
> > Please consider the environment. Do you really need to print this email?
> > 
> > The University of Dundee is a registered Scottish charity, No: SC015096
> > 
> > ___
> > The Galaxy User list should be used for the discussion of
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> > 
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> > 
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> > please use the interface at:
> > 
> >  http://lists.bx.psu.edu/
> 
> 
> The University of Dundee is a registered Scottish charity, No: SC015096
> 


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Re: [galaxy-user] Lastz

[Nate Coraor]

On Nov 11, 2011, at 9:21 AM, Andrew South wrote:

> Hello folks
>  
>  Anyone else having trouble with running Lastz to map?
>  
>  Jobs are being sent but not running.
>  
>  It stopped working for me two days ago after working perfectly, I've tried 
> fiddling with the formats but no joy.

Hi Andy,

It looks like there's a problem with the cluster that runs our NGS jobs.  I'm 
currently looking into it.  Sorry for the inconvenience.

--nate

>  
> Thanks,
> 
> Andy
>  
>  
> Dr A P South 
> Centre for Oncology and Molecular Medicine
> University of Dundee
> Ninewells Hospital & Medical School
> Dundee
> DD1 9SY
> Tel 01382 496432
> Fax 01382 633952
>  
> a.p.so...@dundee.ac.uk
>  
>  
> 
> Please consider the environment. Do you really need to print this email?
> 
> The University of Dundee is a registered Scottish charity, No: SC015096
> 
> ___
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Re: [galaxy-user] Data gets deleted from public server

[Nate Coraor]

On Nov 7, 2011, at 7:11 PM, shamsher jagat wrote:

> I uploaded two BAM files and was working with them but when I tried to use 
> them again they are automatically deleted along with all the steps of 
> analysis?
> Any reason or I am missing something.

Hi Shamsher,

Were you logged in when you performed this analysis?

--nate

> 
> Shamsher
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Re: [galaxy-user] permanently delete problem

[Nate Coraor]

Great, thanks for letting us know.

Richard Mark White wrote:
> actually, i just waited a bit and now they are deletd.
> r
> 
> 
> 
> 
> ____
> From: Nate Coraor 
> To: Richard Mark White 
> Cc: GANDRILLON OLIVIER ; 
> "galaxy-u...@bx.psu.edu" 
> Sent: Wednesday, October 26, 2011 12:55 PM
> Subject: Re: permanently delete problem
> 
> Richard Mark White wrote:
> > hi,
> >   so i went to options-->saved history-->advanced-->deleted datasets.  then 
> > checked all of them, and then hit "permanently delete".
> > but nothign happened.  they still show up as deleted, and they are taking 
> > up lots of my quota.
> > how do i get rid of these?
> > 
> > rich
> 
> Hi Rich,
> 
> I'm not sure what's going on here, I'm looking in to it.
> 
> --nate
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Re: [galaxy-user] permanently delete problem

[Nate Coraor]

Richard Mark White wrote:
> hi,
>   so i went to options-->saved history-->advanced-->deleted datasets.  then 
> checked all of them, and then hit "permanently delete".
> but nothign happened.  they still show up as deleted, and they are taking up 
> lots of my quota.
> how do i get rid of these?
> 
> rich

Hi Rich,

I'm not sure what's going on here, I'm looking in to it.

--nate
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Re: [galaxy-user] Over disk quota

[Nate Coraor]

GANDRILLON OLIVIER wrote:
> Hello
> 
> I just received the following message while using Galaxy through the web
> 
> "You are over your disk quota. Tool execution is on hold until your disk 
> usage drops below your allocated quota."
> 
> I deleted a couple of files but it didn't helped.
> I checked the FAQ and could not get the answer.

Hi Olivier,

The FAQ page is out of date and we'll be updating this as soon as
possible.  Please see the following for information about how to free up
disk space:

http://wiki.g2.bx.psu.edu/Main
http://wiki.g2.bx.psu.edu/Learn/Managing%20Datasets

Sorry for the inconvenience, and thanks for using Galaxy.

--nate

> 
> Thank's for your help
> 
> Olivier
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Re: [galaxy-user] reducing size on disk to comply with quotas

[Nate Coraor]

Patrick Kenneth Gonzales wrote:
> Hi, I am currently using 636gb of storage and would like to reduce it. I have 
> deleted (from disk) most of the datasets in my history. All I've kept are the 
> Bam files which are around 2.7gb each . Unfortunately, the "size on Disk" 
> reads 448.5gb in my saved histories window. It is my understanding that 
> permanently deleted datasets are not considered in quotas. Also, I don't  
> have any copies of these datasets. Where is the 448.5gb of data coming from 
> and how can I get rid of the phantom gb's while keeping the bam files?

Hi Patrick,

Could you provide me with your Galaxy email address off-list?  It
doesn't appear to be the one you sent this email from.  I'll take a look
to make sure Galaxy is correctly calculating your disk usage.

If it's correct, have a look at your saved histories, click "Advanced
Search" and then "deleted", it's possible that the extra data is here.

Thanks,
--nate

> Thanks, Patrick
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Re: [galaxy-user] Injecting External File References

[Nate Coraor]

Oren Livne wrote:
> Dear All,
> 
> We have a lot of sequencing data files whose locations and
> identifiers are managed by our home-grown webapp. We'd like to
> enable users to single-sign-on from our webapp into Galaxy (we will
> be using open ID on both systems for that). When the user opens a
> Galaxy window, we'd like them to be able to access the data files on
> our system which they have permissions to see.
> 
> How should we go about that without copying or moving files? Should
> we make a new data library, or (preferably) create our identifier
> service and make it a remote data source/library that galaxy can see
> and that can be browsed like other data libraries? Is there an API
> we should write our service against, or wrap files with appropriate
> galaxy meta data, etc.?

Hi Oren,

Without knowing the full architecture it's a bit hard to say what the
best solution is.  However, Galaxy's API does allow for "upload" from
locations on the filesystem or from an FTP/HTTP/HTTPS url to a data
library, so you should be able to use this to do what you're talking
about.

Thanks,
--nate

> 
> Thank you so much,
> Oren
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Re: [galaxy-user] Galaxy Architecture Documentation

[Nate Coraor]

Oren,

I do believe some folks have done this, I am a bit surprised none have
replied.  But yes, since Condor supports DRMAA, you should be able to
point $DRMAA_LIBRARY_PATH at Condor's libdrmaa.so, enable the drmaa
runner, and try it out.

--nate

Oren Livne wrote:
> Dear Dave, Victor,
> Is it possible to simply use the drmma job runner with the condor
> drmma lib.so?
> Thanks!
> Oren
> 
> On 9/22/2011 3:21 PM, Victor Ruotti wrote:
> >Hi Dave,
> >That was me!
> >I'm currently talking with the condor folks here in Madison WI.
> >It would be great to get galaxy going with Condor since condor
> >nows forms part of red hat.
> >
> >Besides the existing available docs that you listed below who do
> >you think would be best as a contact for questions regarding this
> >implementation?
> >best,
> >Victor
> >
> >On Sep 21, 2011, at 12:16 PM, Dave Clements wrote:
> >
> >>Hi Oren,
> >>
> >>I had no idea so I went to the Galaxy mailing list archive @
> >>Nabble (http://gmod.827538.n3.nabble.com/Galaxy-f829901.html)
> >>and searched for Condor 
> >>(http://gmod.827538.n3.nabble.com/template/NamlServlet.jtp?macro=search_page&node=829901&query=condor
> >> 
> >>).
> >>It appears that Ravi Madduri @ Argonne has done some work with
> >>this.
> >>
> >>I was also at a meeting in March with someone from Wisconsin
> >>(where I think Condor is currently developed) and they indicated
> >>their might be interest in helping Galaxy work with Condor.
> >>I/you can pursue this option as well.
> >>
> >>Dave C.
> >>
> >>
> >>
> >>
> >>
> >>On Wed, Sep 21, 2011 at 9:38 AM, Oren Livne  >>> wrote:
> >>
> >>Dear Dave,
> >>
> >>This was very useful. Thank you so much. Specifically, I am
> >>trying to integrate Galaxy with Condor, which supports DRMAA. Is
> >>there an existing Condor job runner implementation, or any useful
> >>code for submitting Galaxy jobs to Condor?
> >>
> >>Thanks!
> >>
> >>Oren
> >>
> >>On 9/20/2011 12:21 PM, Dave Clements wrote:
> >>>Hi Oren,
> >>>
> >>>This book chapter
> >>>
> >>> http://userwww.service.emory.edu/~eafgan/content/Galaxy_eScienceGateway.pdf
> >>>
> >>> ,
> >>>includes a high-level overview of Galaxy.  (Note: that chapter
> >>>will be copied to the wiki soon.)
> >>>
> >>>There is some API documentation.
> >>>~/scripts/api/README,
> >>>~/scripts/api/workflow_
> >>>execute.py and
> >>>~/scripts/api/example_watch_folder.py  in the distribution
> >>>
> >>> http://wiki.g2.bx.psu.edu/News%20Briefs/2010_07_16#Initial_implementation_of_the_Galaxy_Web_API
> >>>http://wiki.g2.bx.psu.edu/News%20Briefs/2011_08_30#API
> >>>http://wiki.g2.bx.psu.edu/Events/GCC2011 (/Galaxy Deployment and
> >>>API/ presentation)
> >>>http://wiki.g2.bx.psu.edu/Admin/Sample%20Tracking/Next%20Gen
> >>>http://wiki.g2.bx.psu.edu/Events/GCC2011/Workflows%20and%20API
> >>>
> >>>Sometime in the next week I'll compile all this into a single
> >>>wiki page.
> >>>
> >>>As far as I know there is no "How to write a runner for Galaxy"
> >>>document.  The closest we have is
> >>>http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster and
> >>>
> >>> http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling
> >>>
> >>>Hope this helps,
> >>>
> >>>Dave C.
> >>>
> >>>
> >>>On Mon, Sep 19, 2011 at 9:51 AM, Oren Livne  >>>> wrote:
> >>>
> >>>Dear All,
> >>>
> >>>I am a software developer, new to Galaxy. Is there a
> >>>detailed document about the Galaxy code architecture, API,
> >>>what runners are, and how to write a runner?
> >>>
> >>>I am especially interested in integrating Galaxy with an
> >>>external scheduler software (I am aware of Galaxy's
> >>>scheduling capabilities). I'd like to intercept Galaxy
> >>>workflows and send their object model to my scheduler. I
> >>>could not find this information on the Galaxy Wiki.
> >>>
> >>>Thank you so much in advance,
> >>>Oren Livne
> >>>___
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> >>>Galaxy analysis and other features on the public server
> >>>at usegalaxy.org .  Please keep all
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> >>>using "reply all" in your mail client.  For discussion of
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> >>>
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> >>>
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> >>>
> >>>  

[galaxy-user] Data changes on usegalaxy.org

[Nate Coraor]

Dear Galaxy Users:

The usage of our public site is growing exponentially. As a result, we
are starting to implement new functionality that will allow users to
gauge the size of their datasets and histories. While most changes will
be transparent, you may notice some slight change in history behavior
stemming from this refactoring process. Here's what you might notice and
how deal with it:

- Some of the datasets you've previously deleted may be resurrected in
  your history. Simply re-delete them if you see this happening.

- You may also find that necessary metadata files are missing when you
  use a dataset as a tool input.  These metadata files can be
  regenerated using the "Auto-detect" button on the dataset's "Edit
  Attributes" page, accessible by clicking the dataset's pencil icon.

Thank you for using Galaxy!

--nate
Galaxy Team
http://usegalaxy.org/
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Re: [galaxy-user] temporary files

[Nate Coraor]

Christopher Schroeder wrote:
> Dear all,
> 
> we extended the galaxy functionality with a couple of smaller custom
> scripts. Now we are in the need of some tmpFiles, since our data is
> getting bigger. As far as I understand galaxy by now there might be
> several options:
> 
> - job_working_directory (all "normal" files generated by the job,
> deleted upon completion of  job - safe?)
> - tmp-folder within the database folder (custom path in universe_wsgi.ini?)
> - system-tmp-folder (e.g. samtools-wraper -> only very limited space
> on this harddisk)
> 
> What is the best way to store temporary data in Galaxy (that can be
> deleted after job completion)?

Hi Chris,

It's really up to your personal preference.  In the past we've used all
three.  In general, if the filesystem your job_working_directory resides
in is suitable, it is probably the easiest choice since you get free
cleanup on job completion.

--nate

> 
> Thank you in advance for your help!
> Chris
> 
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Re: [galaxy-user] [galaxy-dev] input security validation

[Nate Coraor]

Roman Valls wrote:
> Sorry for the cross-posting, but I guess that's also interesting to
> Galaxy users...
> 
> I've been thinking about input validation too... only a bit more
> generally, on a server/production basis. Nate, on your production
> setup[1] (galaxy main), do you use any kind of filter or framework a la
> modsecurity[2] to prevent security issues on third party tools ? How do
> you mitigate those security risks ?

Hi Roman,

We don't run modsecurity because we don't run Apache, but tools do
perform input validation, and parameters are santized of any shell
special characters.  In addition, tools only have write access to their
own datasets and working directory.

--nate

> 
> [1] http://usegalaxy.org/production
> [2] http://modsecurity.org/
> 
> On 2011-06-23 00:27, Jennifer Jackson wrote:
> > Hi Russell,
> > 
> > Dan Blankenberg is our ChIP-seq expert and will be able to work with you
> > when he returns from vacation.
> > 
> > Thank you for your patience!
> > 
> > Best,
> > 
> > Jen
> > Galaxy team
> > 
> > On 6/20/11 2:22 PM, Russell Bonneville wrote:
> >> Hello all,
> >>
> >> I am Russell, a student working with Dr. Victor Jin at the Dept. of
> >> Biomedical Informatics, OSU Medical Center. I am developing a Galaxy
> >> wrapper for our ChIP-seq peak-calling program BELT (PMID: 21138948), and
> >> I have a question about input validation. Does Galaxy filter for
> >> malicious field entries (such as XSS attacks) or is this our wrapper’s
> >> responsibility (the MACS wrapper appears to not perform any explicit
> >> checks)? Thank you for your time.
> >>
> >> Sincerely, Russell Bonneville
> >>
> >>
> >>
> >> ___
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> >> in your mail client.  To manage your subscriptions to this
> >> and other Galaxy lists, please use the interface at:
> >>
> >>http://lists.bx.psu.edu/
> > 
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Re: [galaxy-user] FTP and command line access in Galaxy

[Nate Coraor]

Peter Cock wrote:
> On Wed, Jun 22, 2011 at 6:47 AM, Robert Curtis Hendrickson
>  wrote:
> > Nate,
> >
> >
> >
> > The Galaxy’s ability to pull files with user/password from FTP sites as a
> > client is great.
> >
> > However, I need to pull data from an HTTP site at a sequencing center with
> > user/password (already tried to get them to set up an FTP server, no luck).
> > Any way to do this?
> >
> 
> Try asking the sequencing centre if the username and password can be
> provided as part of the HTTP URL, then give that URL to Galaxy.

If it's using HTTP Authentication, the URL is the same as with ftp:

  http://user:h...@example.org/file.ext

Other authentication systems which use forms and cookies or similar
methods won't work.

--nate

> 
> Peter
> 
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Re: [galaxy-user] Unable to load FASTA files?

[Nate Coraor]

Hi,

The cluster resource manager unexpectedly died.  Everything should be
working again after a restart.  Please let us know if you're still
experiencing any problems, and thanks for using Galaxy.

--nate

Nicola Nadeau wrote:
> I've been getting the same error when trying to run Picard, Mark
> Duplicat Reads. Maybe Galaxy is having memory issues?
> 
> Nicola
> 
> On 27/06/2011 13:09, Laura Elizabeth Spoor wrote:
> >Is anyone else having trouble uploading FASTA files to the Galaxy server?
> >
> >I thought it was my files at first, but I have since tried to upload
> >other FASTA files that I have previously had no trouble uploading and I
> >get the same error reported in the info section when I click on the pen
> >icon:
> >
> >Unable to queue job for execution. Resubmitting the job may succeed.
> >
> >(Unfortunately re-submitting the job does not succeed!).
> >
> >The file is 50 MB in size.
> >
> >Any help is greatly appreciated as I am unable to progress my work until
> >this problem is corrected.
> >
> >Best Wishes,
> >
> >Laura
> >
> >
> >
> 
> -- 
> Dr Nicola Nadeau
> Butterfly Genetics Group
> Department of Zoology
> University of Cambridge
> Downing Street
> Cambridge, CB2 3EJ
> Phone: 01223 336644
> Email: nj...@cam.ac.uk
> Web: http://heliconius.zoo.cam.ac.uk/2009/nicola-nadeau/
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Re: [galaxy-user] cuffcompare error in galaxy

[Nate Coraor]

Hi Carlos,

We're expecting to release a stable distribution this week, but you are
always free to pull changes from the central repository.  The suggested
method would be to just pull all changesets up to the one you want, or
up to the tip changeset.

It's not trivial to pull single changesets, you have to export them from
central, import them to your local repository, and then you'll have to
merge when we release a new stable distribution.

--nate

Carlos Javier Borroto wrote:
> I see there is this changeset:
> https://bitbucket.org/galaxy/galaxy-central/changeset/f4b98c453389
> 
> As I have cufflinks 1.0.3, I wonder if this is the cause of the error.
> Maybe I should move to galaxy-central if I want to use cufflinks. Is
> there any clean way to backport a changeset from -central to -dist?
> 
> Thanks,
> --
> Carlos Borroto
> Baltimore, MD
> 
> 
> 
> On Mon, Jun 20, 2011 at 2:01 PM, Carlos Javier Borroto
>  wrote:
> > Hi John,
> >
> > I'm finding the exact same error while going through Jeremy's tutorial
> > in a local instance of galaxy-dist. I was wonder if you found the
> > solution.
> >
> > I see cuffcompare wrapper outputs these files:
> > cc_output.combined.gtf
> > cc_output.input1.refmap
> > cc_output.input1.tmap
> > cc_output.loci
> > cc_output.stats
> > cc_output.tracking
> >
> > and in the logs I'm seing this:
> > galaxy.jobs DEBUG 2011-06-20 13:34:49,902 finish(): Could not move
> > /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output
> > to /home/galaxy/galaxy_dist/database/files/000/dataset_68.dat as
> > directed by from_work_dir
> > galaxy.jobs DEBUG 2011-06-20 13:34:49,917 finish(): Could not move
> > /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.tmap
> > to /home/galaxy/galaxy_dist/database/files/000/dataset_69.dat as
> > directed by from_work_dir
> > galaxy.jobs DEBUG 2011-06-20 13:34:49,932 finish(): Could not move
> > /home/galaxy/galaxy_dist/database/job_working_directory/47/input1.refmap
> > to /home/galaxy/galaxy_dist/database/files/000/dataset_70.dat as
> > directed by from_work_dir
> > galaxy.jobs DEBUG 2011-06-20 13:34:49,948 finish(): Moved
> > /home/galaxy/galaxy_dist/database/job_working_directory/47/cc_output.combined.gtf
> > to /home/galaxy/galaxy_dist/database/files/000/dataset_71.dat as
> > directed by from_work_dir
> >
> > Only cc_output.combined.gtf is correctly being moved, the rest aren't
> > being call by the correct filenames.
> >
> > Thanks,
> > --
> > Carlos Borroto
> > Baltimore, MD
> >
> >
> >
> > 2011/6/10 吳正華 :
> >> Dear galaxy team:
> >>
> >>
> >>
> >> I was testing local galaxy of our lab by analyzing RNA-seq data in Jeremy’s
> >> RNA-seq tutorial.
> >>
> >>
> >>
> >> http://main.g2.bx.psu.edu/u/jeremy/p/galaxy-rna-seq-analysis-exercise
> >>
> >>
> >>
> >> I could run TopHat, cufflinks, and cuffdiff and got results correctly,
> >>
> >> but when I executed cuffcompare through galaxy, the following error
> >> occurred:
> >>
> >>
> >>
> >> Tool execution generated the following error message:
> >>
> >> Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output'
> >>
> >> The tool produced the following additional output:
> >>
> >> cuffcompare v1.0.3 (2403)
> >>
> >> cuffcompare -o cc_output  -s
> >> /home/galaxy/data/galaxy_data/sam_index/hg19.fasta ./input1
> >>
> >>
> >>
> >> and error messages in log file (galaxy.log) are:
> >>
> >>
> >>
> >> galaxy.jobs INFO 2011-06-10 14:02:15,161 job 130 dispatched
> >>
> >> galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:15,466 executing: python
> >> /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py
> >> -s --ref_file="None"
> >> --dbkey=hg19
> >> --index_dir=/home/galaxy/software/galaxy_dist/tool-data
> >> /home/galaxy/software/galaxy_dist/database/files/000/dataset_398.dat
> >>
> >>
> >>
> >> galaxy.jobs.runners.local DEBUG 2011-06-10 14:02:27,834 execution finished:
> >> python
> >> /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py
> >> -s --ref_file="None"
> >>   --dbkey=hg19
> >> --index_dir=/home/galaxy/software/galaxy_dist/tool-data
> >> /home/galaxy/software/galaxy_dist/database/files/000/dataset_398.dat
> >>
> >>
> >>
> >> galaxy.jobs DEBUG 2011-06-10 14:02:27,943 finish(): Could not move
> >> /home/galaxy/software/galaxy_dist/database/job_working_directory/130/cc_output
> >> to /home/galaxy/software/galaxy_dist/database/files/000/dataset_399.dat as
> >> directed by from_work_dir
> >>
> >> galaxy.jobs DEBUG 2011-06-10 14:02:27,971 finish(): Could not move
> >> /home/galaxy/software/galaxy_dist/database/job_working_directory/130/input1.tmap
> >> to /home/galaxy/software/galaxy_dist/database/files/000/dataset_400.dat as
> >> directed by from_work_dir
> >>
> >> galaxy.jobs DEBUG 2011-06-10 14:02:27,999 finish(): Could not move
> >> /home/galaxy/software/galaxy_dist/database/job_working_directory/130/input1.refmap
> >> to /home/galaxy/softwa

Re: [galaxy-user] Galaxy server issues?

[Nate Coraor]

David K Crossman wrote:
> Hello!
> 
> We uploaded 12 samples to Galaxy last night via FTP.  This 
> morning, I went to "Get Data" and clicked on all 12 that were under the FTP 
> location, chose the type of file they were and reference genome and then 
> clicked "Excecute."  The 12 moved over to the History panel and after a 
> couple of minutes went from gray to yellow.  As of this moment, all 12 are 
> still in the yellow stage (still spinning).  Is this normal for that many 
> samples (each sample is about 8GB in size) or should they already have turned 
> green?  Any info would be greatly appreciated.

Hi David,

It's not unlikely for that many files of that size all at once.  I've
checked the PBS queue and your job is still running.

--nate

> 
> Thanks,
> David

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Re: [galaxy-user] galaxy cluster setup

[Nate Coraor]

Robert Jackson wrote:
> Does anyone have practical info on galaxy setup on a cluster?

Hi Robert,

Please see the production server documentation at:

  http://usegalaxy.org/production

--nate

> 
> Robert C. Jackson
> Software Systems Specialist III
> The University of Texas Pan-American
> Computer Support Services
> Division of Information Technology
> Phone: 956-665-2455
> Fax: 956-665-8777
> 

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Re: [galaxy-user] SRMA on a local galaxy instance?

[Nate Coraor]

Gong, Henry wrote:
> 
> Does anyone know how to get SRMA to work properly in galaxy? I've used the 
> pre-built 0.1.15 jar as well as a 0.1.16 jar I built from source, but the 
> result of an SRMA re-alignment job in both instances is a python process 
> which only takes a few percent CPU (or less, since it only seems to be 
> outputting timestamps to the terminal). Here are my system's specs if they're 
> important: 2.8Ghz Intel i5, 4 core; 4GB 1333MHz DDR3; 1TB HDD (430GB free). 
> The OS is OS X 10.6.7. I've also built the required indices and placed them 
> in path/to/galaxy-dist/hg19/srma_path/hg19.dict, hg19.fa.fai, and hg19.fa; 
> the hg19 is a concatenated version of the various chromosome and contig 
> files, and I've followed the sample files in adding these locations to the 
> .loc files (both srma and picard tools).
> 
> The NGS installation page seems to suggest that SRMA does work, so I'm not 
> sure if I'm overreacting, but I'd really appreciate any advice on this, since 
> I imagine others have had similar problems.

Hi Henry,

Where is your srma JAR file located?  It should be
/path/to/galaxy-dist/tool-data/shared/jars/srma.jar

--nate

> 
> Cheers,
> 
> Henry
> 
> 
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Re: [galaxy-user] uploading files via FTP

[Nate Coraor]

somy ork wrote:
> Hi,
> 
> Am trying to configure galaxy to enable file upload via FTP.
> My server is configured with SFTP. and not FTP.
> Will this create a problem in galaxy? coz all my input files are above 2 GB.
> Should i change any settings in the universe_wsgi.ini file?
> Please guide me.

Hi Somy,

SFTP is fine for your local site, I really need to just generalize those
configuration options and the wording so that is not specific to FTP.
The same code can actually just be used to provide access to local
directories that users can copy data into via whatever means is most
appropriate for their own site.

--nate

> 
> Regards
> somy.

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Re: [galaxy-user] Galaxy tool error report from joh...@ibms.sinica.edu.tw

[Nate Coraor]

Hello,

Please don't set your bug report address (error_email_to in
universe_wsgi.ini) to the user mailing list.  This should be set to a
local address at your site.

--nate

galaxy-user@lists.bx.psu.edu wrote:
> 
> GALAXY TOOL ERROR REPORT
> 
> 
> This error report was sent from the Galaxy instance hosted on the server
> "192.168.0.36:8080"
> -
> This is in reference to dataset id 377 from history id 2
> -
> You should be able to view the history containing the related history item
> 
> 176: Cuffcompare on data 175: transcript accuracy 
> 
> by logging in as a Galaxy admin user to the Galaxy instance referenced above
> and pointing your browser to the following link.
> 
> 192.168.0.36:8080/history/view?id=f597429621d6eb2b
> -
> The user 'joh...@ibms.sinica.edu.tw' provided the following information:
> 
> While executing cuffcompare, I encountered this error message:
> 
> Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output'
> 
> I was practicing RNA-seq analysis steps on newly installed galaxy to test if 
> i could easily analyze my data.
> 
> I could run cufflinks and cuffdiff through galaxy, but i'm unable to run 
> cuffcompare.
> 
> how should i solve this problem?
> 
> thanks a lot!
> -
> job id: 126
> tool id: cuffcompare
> -
> job command line:
> python /home/galaxy/software/galaxy_dist/tools/ngs_rna/cuffcompare_wrapper.py 
> -s 
> --ref_file="None" --dbkey=hg19  
> --index_dir=/home/galaxy/software/galaxy_dist/tool-data   
>/home/galaxy/software/galaxy_dist/database/files/000/dataset_376.dat 
> -
> job stderr:
> Error running cuffcompare. [Errno 2] No such file or directory: 'cc_output'
> 
> -
> job stdout:
> cuffcompare v1.0.3 (2403)
> cuffcompare -o cc_output  -s /home/galaxy/data/galaxy_data/sam_index/hg19.fa 
> ./input1 
> 
> -
> job info:
> None
> -
> job traceback:
> None
> -
> (This is an automated message).
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Re: [galaxy-user] Loading files to local Galaxy

[Nate Coraor]

Tilahun Abebe wrote:
> Thank you Paul and Nate. We will try the options you suggested.
> 
> One thing we found to work much faster (less than 5 minutes for most
> files) is to upload zipped data. Galaxy could upload and unzip the
> files without any problem. It doesn't seem any sequence data is
> lost. Has anyone tried this before?

Yes, this is a standard feature.  zip, gzip, and bzip2 are all
supported.  Only one file per archive at this time, however.

--nate

> 
> Thanks.
> 
> Tilahun
> ---
> 
> Nate Coraor wrote:
> >Paul-Michael Agapow wrote:
> >>>From: Tilahun Abebe
> >>>
> >>>We are trying to load Illumina data to our local Galaxy instance. The
> >>>files are between 700 MB and 2.2 GB. Files below 2 GB load in less
> >>than
> >>>5 minutes. Files larger than 2 GB don't upload at all. We installed
> >>>Galaxy locally because we thought loading files will be faster than
> >>the
> >>>server version. Any suggestions to solve this problem is highly
> >>appreciated.
> >>
> >>While  (from others experience) Galaxy _should_ be able to upload files
> >>that large, we've had some problems with our local installation too.
> >>Investigation didn't reveal any cause, so we put it down to the quality
> >>of our network. You might what to look at the webserver or proxy that
> >>you have in front of Galaxy - from memory, both Apache and nginx can be
> >>configured to impose file size limits, so that _may_ be the problem. In
> >>any event, you might want to configure your server to handle uploads and
> >>downloads directly as per
> >><https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServe
> >>r>. Finally you can pass an url to the upload dialog to get Galaxy to
> >>pull the file from an ftp server - for example - and that may prove more
> >>robust.
> >Hi Paul,
> >
> >These failures may be due to the fact that many browsers will simply
> >fail to upload files>  2GB (although I know there are people out there
> >have successfully done it).
> >
> >Tilahun, I'll echo Paul's suggestion to use the Production setup.  There
> >are also alternative options for getting data into Galaxy.  For users,
> >you can have an FTP server (or just a local directory on the server
> >where they can place files for upload):
> >
> >   https://bitbucket.org/galaxy/galaxy-central/wiki/Config/UploadViaFTP
> >
> >Or you can use data libraries and load directly off filesystems
> >accessible to the server:
> >
> >   
> > https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles
> >
> >--nate
> >
> >>
> >>Paul Agapow (paul-michael.aga...@hpa.org.uk)
> >>Bioinformatics, Centre for Infections, Health Protection Agency
> >>
> >>
> >>-
> >>**
> >>The information contained in the EMail and any attachments is
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> >>the named addressee(s). It may not be disclosed to any other person
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> >>recipient, or both. If you are not the intended recipient, you must
> >>not disclose, copy, distribute or retain this message or any part
> >>of it. This footnote also confirms that this EMail has been swept
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> >>
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Re: [galaxy-user] Loading files to local Galaxy

[Nate Coraor]

Paul-Michael Agapow wrote:
> > From: Tilahun Abebe 
> > 
> > We are trying to load Illumina data to our local Galaxy instance. The 
> > files are between 700 MB and 2.2 GB. Files below 2 GB load in less
> than 
> > 5 minutes. Files larger than 2 GB don't upload at all. We installed 
> > Galaxy locally because we thought loading files will be faster than
> the 
> > server version. Any suggestions to solve this problem is highly
> appreciated.
> 
> While  (from others experience) Galaxy _should_ be able to upload files
> that large, we've had some problems with our local installation too.
> Investigation didn't reveal any cause, so we put it down to the quality
> of our network. You might what to look at the webserver or proxy that
> you have in front of Galaxy - from memory, both Apache and nginx can be
> configured to impose file size limits, so that _may_ be the problem. In
> any event, you might want to configure your server to handle uploads and
> downloads directly as per
>  r>. Finally you can pass an url to the upload dialog to get Galaxy to
> pull the file from an ftp server - for example - and that may prove more
> robust.

Hi Paul,

These failures may be due to the fact that many browsers will simply
fail to upload files > 2GB (although I know there are people out there
have successfully done it).

Tilahun, I'll echo Paul's suggestion to use the Production setup.  There
are also alternative options for getting data into Galaxy.  For users,
you can have an FTP server (or just a local directory on the server
where they can place files for upload):

  https://bitbucket.org/galaxy/galaxy-central/wiki/Config/UploadViaFTP

Or you can use data libraries and load directly off filesystems
accessible to the server:

  https://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/UploadingFiles

--nate

> 
> 
> Paul Agapow (paul-michael.aga...@hpa.org.uk)
> Bioinformatics, Centre for Infections, Health Protection Agency
> 
> 
> -
> **
> The information contained in the EMail and any attachments is
> confidential and intended solely and for the attention and use of
> the named addressee(s). It may not be disclosed to any other person
> without the express authority of the HPA, or the intended
> recipient, or both. If you are not the intended recipient, you must
> not disclose, copy, distribute or retain this message or any part
> of it. This footnote also confirms that this EMail has been swept
> for computer viruses, but please re-sweep any attachments before
> opening or saving. HTTP://www.HPA.org.uk
> **
> 
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Re: [galaxy-user] Most Popular Linux flavour for Galaxy

[Nate Coraor]

Matloob Khushi wrote:
> Hello Galaxy Users
> 
> We are anticipating setting up a local instance of Galaxy and wondering what 
> is the most popular (or best) flavour of Linux people out there using. 
> 
> I wonder which OS on UseGalaxy.org has been used. Thanks for your help.

Hi Matloob,

The public Galaxy server runs Solaris 10.  The tools run on two
clusters, one running Debian Squeeze and the other running RHEL 5.6,
both amd64.

You might find that a specialized distribution like BioLinux or
Scientific Linux may pre-package many of the tools you're interested in,
which would make setup a bit easier.

--nate

> 
> Regards
> Matloob
> PhD Candidate

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Re: [galaxy-user] Flagstat crashes in non-linear workflows with TORQUE

[Nate Coraor]

Louise-Amélie Schmitt wrote:
> Le 06/04/2011 13:57, Nate Coraor a écrit :
> >Louise-Amélie Schmitt wrote:
> >>Hello everyone
> >>
> >>I observed an issue when flagstat is incorporated in a workflow in which
> >>the BAM file it works on is also used by another program (generate
> >>pileup for instance) and is NOT the input dataset (generated by sam to
> >>bam within the workflow).
> >>
> >>I tested it with the local job runner and with TORQUE (with the pbs
> >>scheduler and Maui).
> >>
> >>- With the local job runner, it works just fine
> >>
> >>- With TORQUE I get the following error message:
> >>pbs_submit failed, PBS error 15033: No free connections
> >Hi,
> >
> >This can most likely be fixed by increasing the value of NCONNECTS in
> >the TORQUE source, in src/include/libpbs.h, and recompiling on your
> >TORQUE server.  I haven't seen a problem after increasing the value to
> >20.
> >
> >--nate
> >
> Hi,
> 
> Sorry this is old but I tried recompiling torque after setting the
> NCONNECTS to 20 and the issue's still there.
> 
> But there's more: It doesn't affect only flagstat but other
> non-linear workflows. One of the two jobs that are submitted when
> their "father" stopped running triggers the same error:
> PBS error 15033: No free connections

Did you recompile both the client and the server?  I am not sure which
needs it, possibly both.

> 
> And the best part is that it works fine sometimes. But when it
> crashes, it's always the same job that crashes.
> 
> Does anyone have a clue?
> 
> Cheers,
> L-A
> >>Surprisingly, other non-linear workflows work fine. I only observed this
> >>error with flagstat. Moreover, when flagstat is in a linear workflow, it
> >>works fine too. Ad if it is non-linear but the input dataset is the bam
> >>file flagstat works on, it works fine too.
> >>
> >>Please find attached one of the test workflow where I found the error.
> >>The input dataset is a sam file.
> >>
> >>Any clue?
> >>
> >>Cheers,
> >>LA
> >>{
> >> "a_galaxy_workflow": "true",
> >> "annotation": "to see if it fails if not forked",
> >> "format-version": "0.1",
> >> "name": "test flagstat",
> >> "steps": {
> >> "0": {
> >> "annotation": "",
> >> "id": 0,
> >> "input_connections": {},
> >> "inputs": [
> >> {
> >> "description": "",
> >> "name": "Input Dataset"
> >> }
> >> ],
> >> "name": "Input dataset",
> >> "outputs": [],
> >> "position": {
> >> "left": 200,
> >> "top": 200
> >> },
> >> "tool_errors": null,
> >> "tool_id": null,
> >> "tool_state": "{\"name\": \"Input Dataset\"}",
> >> "tool_version": null,
> >> "type": "data_input",
> >> "user_outputs": []
> >> },
> >> "1": {
> >> "annotation": "",
> >> "id": 1,
> >> "input_connections": {
> >> "source|input1": {
> >> "id": 0,
> >> "output_name": "output"
> >> }
> >> },
> >> "inputs": [],
> >> "name": "SAM-to-BAM",
> >> "outputs": [
> >> {
> >> "name": "output1",
> >> "type": "bam"
> >> }
> >> ],
> >> "position": {
> >> "left": 274.5,
> >> "top": 307
> >> },
> >

Re: [galaxy-user] suggestion for multithreading

[Nate Coraor]

Louise-Amélie Schmitt wrote:
> Le 02/06/2011 21:39, Nate Coraor a écrit :
> >Louise-Amélie Schmitt wrote:
> >>>default_cluster_job_runner will remain for backwards compatibility, but
> >>>we'll ship a sample job_conf.xml that runs everything locally by
> >>>default.
> >>>
> >>>--nate
> >>Haha, and I did that before realizing I could do just what I needed by
> >>writing tool-specific pbs:// URLs at the end of the config file... I'm such
> >>an idiot.
> >Haha, okay, I don't think i even noticed since I was distracted by your
> >implementation being a step in the way we want to go with it.
> >
> damn, I shouldn't have said anything :D
> >>But I really like what you did of it and I have a couple of questions.
> >>
> >>Concerning the single-threaded tools, what would happen if the number of
> >>threads set in the xml file was>1 ?
> >It'd consume extra slots, but the tool itself would just run as usual.
> >
> So what about an attribute in the tool tag that would notify wether
> the tool is actually multithreaded, so that this doesn't happen?
> Something like multithreaded="true/false" ?

I'm not sure if it's something we need to enforce (who knows, maybe I
have some reason for having a single-threaded tool reserve multiple
slots), but I do think there should be some way for tool authors to make
it known that their tool is multithreaded.

--nate

> >>Could it be possible to forbid a tool to run on a given node?
> >Hrm.  In PBS you could do it using node properties/neednodes or resource
> >requirements.  I'd have to think a bit about how to do this in a more
> >general way in the XML.
> >
> >--nate
> >
> Ok thank you! :)
> 
> L-A
> >>Thanks,
> >>L-A
> >>
> >>
> >>>>Peter
> >>>>
> 
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Re: [galaxy-user] suggestion for multithreading

[Nate Coraor]

Louise-Amélie Schmitt wrote:
> > 
> > default_cluster_job_runner will remain for backwards compatibility, but
> > we'll ship a sample job_conf.xml that runs everything locally by
> > default.
> > 
> > --nate
> 
> Haha, and I did that before realizing I could do just what I needed by
> writing tool-specific pbs:// URLs at the end of the config file... I'm such
> an idiot.

Haha, okay, I don't think i even noticed since I was distracted by your
implementation being a step in the way we want to go with it.

> But I really like what you did of it and I have a couple of questions.
> 
> Concerning the single-threaded tools, what would happen if the number of
> threads set in the xml file was >1 ? 

It'd consume extra slots, but the tool itself would just run as usual.

> Could it be possible to forbid a tool to run on a given node?

Hrm.  In PBS you could do it using node properties/neednodes or resource
requirements.  I'd have to think a bit about how to do this in a more
general way in the XML.

--nate

> 
> Thanks,
> L-A
> 
> 
> > 
> >> 
> >> Peter
> >>
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Re: [galaxy-user] suggestion for multithreading

[Nate Coraor]

Peter Cock wrote:
> On Thu, Jun 2, 2011 at 6:23 PM, Nate Coraor  wrote:
> > Peter Cock wrote:
> >> On a related point, I've previously suggested a $variable could be defined
> >> for use in tool XML wrappers to set the number of threads. This number
> >> could come from a general configuration file, or perhaps via the cluster
> >> settings - the point is the tool doesn't need to know, it just gets told 
> >> how
> >> many threads it is allowed.
> >
> > Yeah, that's the idea.
> >
> > job_conf.xml:
> >
> > 
> > 
> >    
> >        
> >        
> >            batch
> >        
> >    
> >    
> >        
> >        
> >            8
> >        
> >    
> > 
> >
> > pbs.py then knows to translate '8' to
> > '-l nodes=1:ppn=8'.
> >
> > Your tool can access that value a bunch, like $__resources__.cores.
> >
> > The same should be possible for other consumables.
> >
> 
> Sounds good. Would there be a global default setting somewhere in
> universe.ini or elsewhere for when job_conf.xml didn't set a value?

default_cluster_job_runner will remain for backwards compatibility, but
we'll ship a sample job_conf.xml that runs everything locally by
default.

--nate

> 
> Peter
> 
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Re: [galaxy-user] suggestion for multithreading

[Nate Coraor]

Peter Cock wrote:
> 2011/6/2 Nate Coraor :
> > Hi Louise-Amélie,
> >
> > I haven't done anything with this code yet, but I wanted to let you know
> > that we'll eventually be adding it, I'm just going to change the
> > implementation slightly.  I'd like to merge the functionality of the csv
> > into an xml config I'm already working on (but haven't yet fully decided
> > on the syntax).  And it should be possible for tools to access these
> > parameters in the command line template.  A lot of our NGS tools have
> > the number of threads to use hardcoded in the tool config, which is bad.
> >
> > --nate
> 
> On a related point, I've previously suggested a $variable could be defined
> for use in tool XML wrappers to set the number of threads. This number
> could come from a general configuration file, or perhaps via the cluster
> settings - the point is the tool doesn't need to know, it just gets told how
> many threads it is allowed.

Yeah, that's the idea.

job_conf.xml:






batch





8




pbs.py then knows to translate '8' to
'-l nodes=1:ppn=8'.

Your tool can access that value a bunch, like $__resources__.cores.

The same should be possible for other consumables.

--nate

> 
> Peter
> 
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Re: [galaxy-user] suggestion for multithreading

[Nate Coraor]

Hi Louise-Amélie,

I haven't done anything with this code yet, but I wanted to let you know
that we'll eventually be adding it, I'm just going to change the
implementation slightly.  I'd like to merge the functionality of the csv
into an xml config I'm already working on (but haven't yet fully decided
on the syntax).  And it should be possible for tools to access these
parameters in the command line template.  A lot of our NGS tools have
the number of threads to use hardcoded in the tool config, which is bad.

--nate

Louise-Amélie Schmitt wrote:
> Just one little fix on line 261:
> 261 if ( len(l) > 1 and l[0] == job_wrapper.tool.id ):
> 
> Otherwise it pathetically crashes when non-multithreaded jobs are
> submitted. Sorry about that.
> 
> Regards,
> L-A
> 
> Le mardi 19 avril 2011 à 14:33 +0200, Louise-Amélie Schmitt a écrit :
> > Hello everyone,
> > 
> > I'm using TORQUE with Galaxy, and we noticed that if a tool is
> > multithreaded, the number of needed cores is not communicated to pbs,
> > leading to job crashes if the required resources are not available when
> > the job is submitted.
> > 
> > Therefore I modified a little the code as follows in
> > lib/galaxy/jobs/runners/pbs.py
> > 
> > 256 # define PBS job options
> > 257 attrs.append( dict( name = pbs.ATTR_N, value = str( "%s_%s_%
> > s" % ( job_wrapper.job_id, job_wrapper.tool.id, job_wrapper.user ) ) ) )
> > 258 mt_file = open('tool-data/multithreading.csv', 'r')
> > 259 for l in mt_file:
> > 260 l = string.split(l)
> > 261 if ( l[0] == job_wrapper.tool.id ):
> > 262 attrs.append( dict( name = pbs.ATTR_l,
> > resource = 'nodes', value = '1:ppn='+str(l[1]) ) )
> > 263 attrs.append( dict( name = pbs.ATTR_l,
> > resource = 'mem', value = str(l[2]) ) )
> > 264 break
> > 265 mt_file.close()
> > 266 job_attrs = pbs.new_attropl( len( attrs ) +
> > len( pbs_options ) )
> > 
> > (sorry it didn't come out very well due to line breaking)
> > 
> > The csv file contains a list of the multithreaded tools, each line
> > containing:
> > \t\t\n
> > 
> > And it works fine, the jobs wait for their turn properly, but
> > information is duplicated. Perhaps there would be a way to include
> > something similar in galaxy's original code (if it is not already the
> > case, I may not be up-to-date) without duplicating data.
> > 
> > I hope that helps :)
> > 
> > Best regards,
> > L-A
> > 
> > ___
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Re: [galaxy-user] biomart error

[Nate Coraor]

You can also only pull the 5589 changeset - this one *just* missed the
stable release (stable is at 5588):

  % hg pull -r 316f79f7bc1a https://bitbucket.org/galaxy/galaxy-central/
  % hg update

--nate

Greg Von Kuster wrote:
> Hi Lisa,
> 
> Very sorry for the confusion - you are correct!  The tip of the galaxy-dist 
> repo at https://bitbucket.org/galaxy/galaxy-dist is change set 5585, so the 
> fix is not available in the dist repo yet, and probably won't be there for 
> another few weeks.  
> 
> If you don't want to wait, you can pull the fix from our development repo at 
> https://bitbucket.org/galaxy/galaxy-central.
> 
> Greg Von Kuster
> 
> 
> On May 31, 2011, at 11:52 AM, Liisa Koski wrote:
> 
> > Hi Greg, 
> > I thought I was up to date. When I run the following command I get 'no 
> > changes found' 
> > 
> > hg incoming 
> > real URL is https://bitbucket.org/galaxy/galaxy-dist 
> > comparing with http://www.bx.psu.edu/hg/galaxy 
> > searching for changes 
> > no changes found 
> > [galaxy@galaxy_dist]$ 
> >   
> > Thanks, 
> > Liisa 
> > 
> > 
> > From:   Greg Von Kuster 
> > To: Liisa Koski 
> > Cc: j...@bx.psu.edu, galaxy-user@lists.bx.psu.edu, 
> > galaxy-user-boun...@lists.bx.psu.edu
> > Date:   2011-05-31 11:29
> > Subject:Re: [galaxy-user] biomart error
> > 
> > 
> > 
> > 
> > Hello Lisa, 
> > 
> > I noticed your stack trace in another message you sent - pasted below.  If 
> > this is the problem you are seeing, then upgrading your Galaxy instance to 
> > the latest version will fix the problem.  This issue was fixed in change 
> > set 5589. 
> > 
> > This is the exact error I am getting... 
> > 
> > Traceback (most recent call last):
> > File "galaxy_dist/lib/galaxy/jobs/runners/local.py", line 58, in run_job
> >   job_wrapper.prepare()
> > File "galaxy_dist/lib/galaxy/jobs/__init__.py", line 361, in prepare
> >   self.tool.exec_before_job( self.queue.app, inp_data, out_data, param_dict 
> > )
> > File "galaxy_dist/lib/galaxy/tools/__init__.py", line 1881, in 
> > exec_before_job
> >   json_params[ 'param_dict' ] = self._prepare_datasource_json_param_dict( 
> > param_dict ) #it would probably be better to store the original incoming 
> > parameters here, instead of the Galaxy modified ones?
> > File "galaxy_dist/lib/galaxy/tools/__init__.py", line 1867, in 
> > _prepare_datasource_json_param_dict
> >   rval[ key ] = self._prepare_datasource_json_list( val )
> > NameError: global name 'val' is not defined 
> > 
> > 
> > 
> > Greg Von Kuster 
> > 
> > 
> > On May 31, 2011, at 11:06 AM, Liisa Koski wrote: 
> > 
> > I am also getting the same error with my local biomart and local galaxy 
> > installations. 
> > 
> > Thanks, 
> > Liisa 
> >  
> > 
> > From:   Jennifer Jackson 
> > To: Christophe Klopp 
> > Cc: galaxy-user@lists.bx.psu.edu
> > Date:   2011-05-31 09:32
> > Subject:Re: [galaxy-user] biomart error
> > Sent by:galaxy-user-boun...@lists.bx.psu.edu
> > 
> > 
> > 
> > 
> > 
> > Hello Christophe,
> > 
> > I am unable to duplicate - BioMart appears to be functioning as expected 
> > this morning. Would you have time to run your query again?
> > 
> > If the problem persists, if you could share your history with me 
> > (Options -> Share or Publish -> email back link) and list out the exact 
> > steps that you are performing, that would be very helpful.
> > 
> > Best,
> > 
> > Jen
> > Galaxy team
> > 
> > On 5/30/11 8:33 AM, Christophe Klopp wrote:
> > > Hi,
> > >
> > > I've tried a simple query in biomart : retrieve all gene locations for
> > > the Danio rerio in Ensembl 62 and I get an error :
> > > An error occurred running this job: /failure preparing job
> > > /
> > > The same happens with the test site?
> > >
> > > Cheers
> > >
> > > Christophe/
> > > /
> > >
> > > --
> > > 
> > > = Christophe KLOPP BIAINRA Toulouse 31326 Castanet-Tolosan =
> > > = Tel: 33 5 61 28 50 36   Email:christophe.kl...@toulouse.inra.fr  =
> > > =http://www.sigenae.org/   =
> > > =http://bioinfo.genotoul.fr/   =
> > > 
> > >
> > >
> > >
> > > ___
> > > 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 Jackson
> > http://usegalaxy.org
> > http://galaxyproject.org
> > _

Re: [galaxy-user] runtime warning with pysam egg

[Nate Coraor]

Shantanu Pavgi wrote:
> 
> Hi,
> 
> I am getting following warning when I start the galaxy server. I am using 
> latest revision (50e249442c5a) of galaxy-dist.  Am I missing anything in the 
> configuration here? 
> 
> {{{
> $ ./run.sh 
>   
> /home/galaxy/.python-eggs/pysam-0.4.1_kanwei_ae2bd50d9945-py2.6-linux-x86_64-ucs2.egg-tmp/csamtools.so:6:
>  RuntimeWarning: __builtin__.file size changed, may indicate binary 
> incompatibility
> ###t#|}###b###S#5#D###i)###[x,m
>
> ###<#=LB###q##.:##$2###rDM###E3A#j###

Hi Shantanu,

This warning is safe to ignore.  I haven't had a chance to look in to
why this occurs, but it does not affect normal Galaxy operation.

--nate

>   python path is: 
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/numpy-1.3.0-py2.6-linux-x86_64-ucs2.egg,
>  
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pysam-0.4.1_kanwei_ae2bd50d9945-py2.6-linux-x86_64-ucs2.egg,
>  /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Whoosh-0.3.18-py2.6.egg, 
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pycrypto-2.0.1-py2.6-linux-x86_64-ucs2.egg,
>  
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs2.egg,
>  
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/bx_python-0.7.0_14b6a6c95da6-py2.6-linux-x86_64-ucs2.egg,
>  /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/amqplib-0.6.1-py2.6.egg, 
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/pexpect-2.4-py2.6.egg, 
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg,/share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Babel-0.9.4-py2.6.egg,
>  /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Beaker-1.4-py2.6.egg, 
> /share/apps/gal!
 ax!
>  y/galaxy-dist-50e249442c5a/eggs/Mako-0.2.5-py2.6.egg, 
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/WebHelpers-0.2-py2.6.egg, 
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs2.egg,
>  /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/wchartype-0.1-py2.6.egg, 
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/elementtree-1.2.6_20050316-py2.6.egg,
>  /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/docutils-0.7-py2.6.egg, 
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/WebOb-0.8.5-py2.6.egg, 
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Routes-1.12.3-py2.6.egg, 
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs2.egg,
>  
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/PasteDeploy-1.3.3-py2.6.egg, 
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/PasteScript-1.7.3-py2.6.egg, 
> /share/apps/galaxy/galaxy-dist-50e249442c5a/eggs/Paste-1.6-py2.6.egg, 
> /share/apps/galaxy/galaxy-dist-50e249442c5a/lib, /share/apps/gal!
 ax!
>  y/python/2.6.6/lib/python26.zip, 
> /share/apps/galaxy/python/2.6.6/lib/python2.6, 
> /share/apps/galaxy/python/2.6.6/lib/python2.6/plat-linux2, 
> /share/apps/galaxy/python/2.6.6/lib/python2.6/lib-tk, 
> /share/apps/galaxy/python/2.6.6/lib/python2.6/lib-old, 
> /share/apps/galaxy/python/2.6.6/lib/python2.6/lib-dynload, 
> /share/apps/galaxy/python/2.6.6/lib/python2.6/site-packages
>   galaxy.datatypes.registry DEBUG 2011-04-25 12:37:54,637 Loading 
> datatypes from datatypes_conf.xml
>   galaxy.datatypes.registry DEBUG 2011-04-25 12:37:54,650 Loaded display 
> application 'ucsc_bam' for datatype 'bam', inherit=False
> ...
> ...
> ...
> 
> }}}
> 
> --
> Thanks,
> Shantanu.
> ___
> 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
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> 
>   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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Re: [galaxy-user] Reload ".loc" files without restarting the Galaxy server?

[Nate Coraor]

Roman Valls wrote:
> On standard UNIX, the SIGHUP signal (kill -HUP ) is used to perform
> this kind of actions (re-read config files) on almost all daemons [1].
> 
> Doing a quick grep:
> 
> $ grep -ri "HUP" galaxy-central
> 
> Nothing shows up, so as Jen indicated, does not seem to be implemented
> at first glance... but one could have a look at:
> 
> http://docs.python.org/library/signal.html
> 
> And handle that signal... I guess that the daemon would be "paster", but
> haven't found where it reads the loc files :-S

I actually implemented SIGHUP and then found that it would not work:

  http://bugs.python.org/issue7978

If that patch actually made it to a 2.6 minor release it may solve the
problem and I could commit this code.

--nate

> 
> 
> [1] http://en.wikipedia.org/wiki/SIGHUP
> 
> On 2011-04-12 22:50, Luobin Yang wrote:
> > Hi all,
> > 
> > I am wondering if it's possible to to reload a ".loc" file without
> > restarting the Galaxy server?
> > 
> > Thanks,
> > Luobin
> > 
> > 
> > 
> > ___
> > 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/
> ___
> 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
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> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
> 
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Re: [galaxy-user] Flagstat crashes in non-linear workflows with TORQUE

[Nate Coraor]

Louise-Amélie Schmitt wrote:
> Hello everyone
> 
> I observed an issue when flagstat is incorporated in a workflow in which
> the BAM file it works on is also used by another program (generate
> pileup for instance) and is NOT the input dataset (generated by sam to
> bam within the workflow).
> 
> I tested it with the local job runner and with TORQUE (with the pbs
> scheduler and Maui).
> 
> - With the local job runner, it works just fine
> 
> - With TORQUE I get the following error message:
> pbs_submit failed, PBS error 15033: No free connections

Hi,

This can most likely be fixed by increasing the value of NCONNECTS in
the TORQUE source, in src/include/libpbs.h, and recompiling on your
TORQUE server.  I haven't seen a problem after increasing the value to
20.

--nate

> 
> Surprisingly, other non-linear workflows work fine. I only observed this
> error with flagstat. Moreover, when flagstat is in a linear workflow, it
> works fine too. Ad if it is non-linear but the input dataset is the bam
> file flagstat works on, it works fine too.
> 
> Please find attached one of the test workflow where I found the error.
> The input dataset is a sam file.
> 
> Any clue?
> 
> Cheers,
> LA

> {
> "a_galaxy_workflow": "true", 
> "annotation": "to see if it fails if not forked", 
> "format-version": "0.1", 
> "name": "test flagstat", 
> "steps": {
> "0": {
> "annotation": "", 
> "id": 0, 
> "input_connections": {}, 
> "inputs": [
> {
> "description": "", 
> "name": "Input Dataset"
> }
> ], 
> "name": "Input dataset", 
> "outputs": [], 
> "position": {
> "left": 200, 
> "top": 200
> }, 
> "tool_errors": null, 
> "tool_id": null, 
> "tool_state": "{\"name\": \"Input Dataset\"}", 
> "tool_version": null, 
> "type": "data_input", 
> "user_outputs": []
> }, 
> "1": {
> "annotation": "", 
> "id": 1, 
> "input_connections": {
> "source|input1": {
> "id": 0, 
> "output_name": "output"
> }
> }, 
> "inputs": [], 
> "name": "SAM-to-BAM", 
> "outputs": [
> {
> "name": "output1", 
> "type": "bam"
> }
> ], 
> "position": {
> "left": 274.5, 
> "top": 307
> }, 
> "tool_errors": null, 
> "tool_id": "sam_to_bam", 
> "tool_state": "{\"source\": \"{\\\"index_source\\\": 
> \\\"cached\\\", \\\"input1\\\": null, \\\"__current_case__\\\": 0}\", 
> \"__page__\": 0}", 
> "tool_version": "1.1.1", 
> "type": "tool", 
> "user_outputs": []
> }, 
> "2": {
> "annotation": "", 
> "id": 2, 
> "input_connections": {
> "input1": {
> "id": 1, 
> "output_name": "output1"
> }
> }, 
> "inputs": [], 
> "name": "flagstat", 
> "outputs": [
> {
> "name": "output1", 
> "type": "txt"
> }
> ], 
> "position": {
> "left": 396.5, 
> "top": 445
> }, 
> "tool_errors": null, 
> "tool_id": "samtools_flagstat", 
> "tool_state": "{\"__page__\": 0, \"input1\": \"null\"}", 
> "tool_version": "1.0.0", 
> "type": "tool", 
> "user_outputs": []
> }, 
> "3": {
> "annotation": "", 
> "id": 3, 
> "input_connections": {
> "refOrHistory|input1": {
> "id": 1, 
> "output_name": "output1"
> }
> }, 
> "inputs": [], 
> "name": "Generate pileup", 
> "outputs": [
> {
> "name": "output1", 
> "type": "tabular"
> }
> ], 
> "position": {
> "left": 519, 
> "top": 340
> }, 
> "tool_errors": null, 
> "tool_id": "sam_pileup", 
> "tool_state": "{\"__page__\": 0, \"c\": \"{\\\"consensus\\\": 
> \\\"no\\\", \\\"__current_case__\\\": 0}\", \"indels\": \"\\\"no\\\"\", 
> \"refOrHistory\": \"{\\\"input1\\\": null, \\\"reference\\\": 
> \\\"indexed\\\", \\\"__current_case__\\\": 0}\", \"lastCol\": \"\\\"no\\\"\", 
> \"mapCap\": \"\\\"60\\\"\"}", 
> "tool_version": "1.1.1", 
> "typ

Re: [galaxy-user] where to get indexes for mapping tools

[Nate Coraor]

Yury Bukhman wrote:
> Hi,
> 
> we have set up a Galaxy server for internal use.  We would like to provide 
> indexes for NGS mapping tools for a set of organisms that are relevant to our 
> research.  While bowtie has a repository of such indexes, other tools, e.g. 
> bwa, don't seem to have one, so we have to build our own.  Is there a 
> repository of pre-built indexes for all mapping tools supported by Galaxy 
> somewhere?

Hi Yury,

We are working on setting up a mirror of all of our reference data that
will be accessible via rsync and possibly http.  There'll be an
announcement when this is available.

--nate

> 
> Thanks.
> 
> Yury
> 
> 
> --
> Yury V. Bukhman, Ph.D.
> Associate Scientist, Bioinformatics
> Great Lakes Bioenergy Research Center
> University of Wisconsin - Madison
> 445 Henry Mall, Rm. 513
> Madison, WI 53706, USA
> Phone: 608-890-2680  Fax: 608-890-2427
> Email: ybukh...@glbrc.wisc.edu
> 
> ___
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> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
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> use the Galaxy Development list:
> 
>   http://lists.bx.psu.edu/listinfo/galaxy-dev
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> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
> 
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Re: [galaxy-user] Galaxy server-FTP

[Nate Coraor]

Sher, Falak wrote:
> Sorry I did not know there is some special software I need to use, could you 
> help please ?

Have you seen the instructions here?:

https://bitbucket.org/galaxy/galaxy-central/wiki/UploadViaFTP

Those example screenshots use Cyberduck.  FileZilla is also a popular
cross-platform FTP client.

--nate

> 
> ____
> From: Nate Coraor [n...@bx.psu.edu]
> Sent: Thursday, March 31, 2011 11:36 PM
> To: Sher, Falak
> Cc: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] Galaxy server-FTP
> 
> Sher, Falak wrote:
> > HI
> > I would like to use Galaxy server to upload files via FTP. I seek help for, 
> > log in to the FTP server at main.g2.bx.psu.edu.
> > I dont see ftp log in option there.
> > help please ?
> 
> Hi Falak,
> 
> What software are you using to try to connect via FTP?
> 
> --nate
> 
> >
> >
> > Falak
> >
> > ___
> > 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
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> >
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> >
> > To manage your subscriptions to this and other Galaxy lists,
> > please use the interface at:
> >
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Re: [galaxy-user] Galaxy server-FTP

[Nate Coraor]

Sher, Falak wrote:
> HI
> I would like to use Galaxy server to upload files via FTP. I seek help for, 
> log in to the FTP server at main.g2.bx.psu.edu.
> I dont see ftp log in option there.
> help please ?

Hi Falak,

What software are you using to try to connect via FTP?

--nate

> 
> 
> Falak
> 
> ___
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Re: [galaxy-user] Galaxy down?

[Nate Coraor]

Felix Hammer wrote:
> Hi, is there currently a problem with the Galaxy Server?
> When will it be up again?

Hi Felix,

There were some problems caused by unusually high load which should now
be resolved.  Jobs are running now, albeit a bit slowly.  Please let us
know if there are any continuing problems.

Thanks,
--nate

> thx, Felix
> 
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Re: [galaxy-user] Export data to filesystem

[Nate Coraor]

James Lindsay wrote:
> Hello,
> I was wondering if there was a way to export a dataset to the file
> system? Basically I think it would be advantageous if someone could
> copy a dataset to an "export" folder, they could then FTP this data
> away or work with it locally?

Hi James,

This doesn't exist currently, although various people have implemented
it as a tool in their own environments, you may want to ask for copies
of such tools over on the Development list.  It's something we plan to
implement more directly in the future.

--nate

> 
> Thanks for the help,
> James
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Re: [galaxy-user] Bowtie Job doesn't start

[Nate Coraor]

Felix Hammer wrote:
> Hi,
> just trying to use Bowtie, but the job does not start.
> Is there somthing wrong with the server at the moment?

Hi Felix,

It looks like the reservation on the cluster which runs bowtie jobs
isn't working at the moment and there's some contention for resources.
I've reported the bug to the folks who maintain this cluster and
hopefully it'll be resolved shortly.

--nate

> Felix
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Re: [galaxy-user] FTP access to Galaxy data?

[Nate Coraor]

Ready, Robert F Jr wrote:
> Greetings,
> 
> I am wondering if there is a way to directly access data sets created and 
> stored on Galaxy. A >50Gb set of raw sequencing results was uploaded via FTP, 
> and is currently being groomed and clipped. Following the clipping, we would 
> like to download a copy to a local cluster for analysis with tools not 
> available on Galaxy.
> 
> The only way I can find to do this is to download via the web interface to a 
> local computer, then copy the data to the cluster. I'd rather not move the 
> data twice if I can help it. Is there a way that I can access Galaxy datasets 
> via the command line on our cluster, perhaps making the data available via 
> FTP, so that I can directly download it to the place it needs to be?

Hi Bob,

If the dataset is public, you can fetch it using wget or curl.  The link
to download can be obtained by right clicking the floppy disk icon
inside a history item and choosing "Copy Link Address."  Once you have
the link:

  % wget ''

or 

  % curl -O ''

The quotes aren't strictly necessary but will prevent the shell from
evaluating the '?' character in the link.

--nate

> 
> Thank you,
> 
> Bob
> 
> --
> Robert Ready
> Undergraduate Research Assistant
> Logsdon Lab
> Department of Biology
> University of Iowa

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Re: [galaxy-user] Installing Galaxy locally

[Nate Coraor]

Kanwei Li wrote:
> Hi David,
> 
> Yes, it is free and easy to set up, and we have instructions here:
> https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy

You may also want to point the tech folks at the following page:

  https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ProductionServer

It's linked at the bottom of the page that Kanwei posted, but it's worth
specific mention since it explains all of the requirements for setting
up a Galaxy server for multi-user, cluster, etc. use.

--nate

> 
> Thanks!
> 
> Kanwei
> 
> On Mon, Feb 21, 2011 at 5:42 PM, David Matthews
> wrote:
> 
> > Hi,
> >
> > I am not a computer person and very much like using Galaxy because its nice
> > and easy for non-bioinformaticians. Tomorrow I am going to have a meeting
> > with the computer science department here at Bristol and I am hoping to
> > persuade them to install Galaxy within the High Performance Computing Centre
> > for University of Bristol users. As I understand it this is relatively
> > straight forward - that is to say the project was designed for them to
> > install the whole thing locally and reproduce the set up here so I and
> > others can use it here instead of clogging up your machines with our data
> > and requests (!). Is this right? There are no fees or anything and this is
> > something most computer centres should be able to do? I know this may seem a
> > silly question but it seems prudent to ask!
> >
> > Cheers
> > David
> >
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> >
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> >

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Re: [galaxy-user] Upload via SCP?

[Nate Coraor]

Felix Hammer wrote:
> Hi,
> is it possible to use SCP to upload files instead of FTP?

Hi Felix,

At this time, no.

--nate

> thxbye,
> Felix
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Re: [galaxy-user] Missing scrollbars on openid page

[Nate Coraor]

Peter wrote:
> Hi all,
> 
> I ran into a small issue with account creation, likely to affect
> people using a netbook or other device with a low (vertical)
> resolution.
> 
> I don't think I have an account on main.g2.bx.psu.edu so I tried using
> OpenID via GoogleMail. This brought me to the following page:
> 
> http://main.g2.bx.psu.edu/user/openid_associate?username=&status=warning&message=OpenID+authentication+was+successful%2C+but+you+need+to+associate+your+OpenID+with+a+Galaxy+account.&use_panels=True&email=
> 
> There are no scroll bars on this page (which usually means the page
> explicitly disabled them), and it is too long to fit on my screen
> without zooming out so much that I can hardly read it. I'm using
> Firefox 3.6 on Linux.

Hi Peter,

Thanks for reporting this issue.  It has been fixed in our code and
should be out on the Main server within a few days.

--nate

> 
> (I then got a username clash, and realised I'd already made an account
> with a different email address)
> 
> Peter
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Re: [galaxy-user] Mapping does not start

[Nate Coraor]

Felix Hammer wrote:
> Hi,
> 
> I am trying to map sequences with Bowtie.
> Have been waiting for a few hours now but it still says "Job is waiting to
> run".
> 
> A few days ago I didn't have this problem and the job started immediately.
> My guess is that the jobs are still stuck in a queue?
> 
> How can I tell when the jobs will approximately start running? Is there a
> way to view the queue position?

Hi Felix,

Unfortunately, the cluster that serves these jobs is temporarily offline
for emergency maintenance.  Estimates are that it will be back up within
a few hours.

--nate

> 
> thx,
> Felix
> 
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Re: [galaxy-user] Downloadable Galaxy Virtual Machine in VMware

[Nate Coraor]

Haarst, Jan van wrote:
> The download can also be done using bittorrent, torrent is available at 
> http://www.biotorrents.net/details.php?id=136 .
> This might be faster, as one of the peers is in Canada.

This is great!  I haven't checked the image out, but I'm fetching the
torrent now and will leave it seeding here from PSU to help out.

Thanks,
--nate

> 
> With kind regards,
> Jan
>  
> 
> > -Original Message-
> > From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-
> > boun...@lists.bx.psu.edu] On Behalf Of Leon Mei
> > Sent: Tuesday, February 01, 2011 1:08 PM
> > To: galaxy-user@lists.bx.psu.edu
> > Cc: David van Enckevort; Rob Hooft
> > Subject: [galaxy-user] Downloadable Galaxy Virtual Machine in VMware
> > 
> > Dear list,
> > 
> > Within the Netherlands Bioinformatics Centre, we have implemented a Galaxy 
> > VM by
> > wrapping up the distributed version from PennState. We are also adding more 
> > easy-to-
> > use pipelines for Genomics and Proteomics data analysis into this server at 
> > the
> > moment.
> > 
> > You can download the current version at: http://bet1.nbiceng.net/galaxy/
> > 
> > More documents can be found at: https://wiki.nbic.nl/index.php/Galaxy_VM
> > 
> > By sharing this VM, we hope to relieve you from the normal installation and
> > configuration steps (sometimes can be difficult) if you want to run a local 
> > Galaxy
> > instance.
> > 
> > If you are interested in this procedure or have questions on that, we are 
> > happy to
> > share our experience and scripts.
> > 
> > Best regards,
> > Leon
> > 
> > --
> > Hailiang (Leon) Mei
> > Netherlands Bioinformatics Center (http://www.nbic.nl/)
> > Skype: leon_mei    Mobile: +31 6 41709231
> > 
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Re: [galaxy-user] Zipping files to download

[Nate Coraor]

Cristian Rojas wrote:
> I would like to know if it is possible zip files in Galaxy before download to 
> my 
> computer. How can I do this?

Hi Cristian,

The "Export to File" feature under the history's "Options" menu will
export the entire history to a compressed tar file which can then be
downloaded.  At present it is not possible to selectively choose
datasets for inclusion/exclusion in this archive.

However, if you download a single file from your history, it will be
compressed by the Galaxy server and decompressed by your browser on the
fly, which means you won't have to transfer the whole file
inefficiently.

--nate

> Thnks.
> Regards,
> Cristian
> 
> 
> 
>   
> 
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