Re: [galaxy-dev] Please help fix toolshed repository: trtr

[Martin Čech]

Hi Lance,

Dave Bouvier removed the unwanted folder on the TS side. (It wasn't ever
tracked by mercurial). You should be ok now.

Sorry for the inconvenience.

Thank you for using Galaxy.

Martin

On Tue, Mar 15, 2016 at 5:41 PM Lance Parsons 
wrote:

> When I clone the repo, I don't see that folder:
>
>hg clone https://toolshed.g2.bx.psu.edu/repos/mrvollger/trtr
>
> Lance
>
> Martin Čech wrote:
>
>
> Hi Lance,
>
> it seems the whole .git/ folder got accidentally uploaded there and it
> causes trouble. I recommend using the direct mercurial access
> (https://toolshed.g2.bx.psu.edu/repos/mrvollger/trtr), delete the
> folder, commit the change and push it to the TS repository.
>
> Please let me know how it goes.
>
> Martin
>
> On Tue, Mar 15, 2016 at 4:54 PM Lance Parsons 
> > wrote:
>
> I was helping someone with their toolshed repository and we ran
> into an issue, there is an old folder "myTools" in the repository
> that we cannot delete. It has a second copy of the tool
> (inadvertently). However, when we upload a new version with
> Planemo, the directory remains. Attempts to delete it via the
> toolshed web interface result in internal server errors. Can an
> admin take a look?
>
> https://toolshed.g2.bx.psu.edu/view/mrvollger/trtr/13cad5d36301
>
>
> --
> Lance Parsons - Scientific Programmer
> Carl C. Icahn Laboratory - Room 136
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
>
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Re: [galaxy-dev] Setting job_working_directory on per-tool basis? (cuffdiff/cummerbund SQLite db error)

[John Chilton]

Yeah - your discoveries are exactly right. 16.04 has added the ability
to configure a bunch of extra things on a per-job-destination basis
but this isn't included yet - probably should be though. Pulsar would
be a way to go - hopefully soon Pulsar will be included with Galaxy
directly and it will be as easy as declaring a new job destination
(https://github.com/galaxyproject/galaxy/issues/1378) but I don't
think that will make it into 16.04.

-John

On Wed, Mar 9, 2016 at 2:41 PM, Peter Briggs
 wrote:
> Just to follow up on my own questions, in case it's of interest to others:
>
> -- Re specifying different job working directories on a per-tool basis:
>
> Having spent a bit of time looking at the "advanced" sample job_conf.xml and
> also at the code for setting up and dispatching jobs, it looks to me like it
> is not possible to do this (i.e. specify different job working directories
> within different job destinations).
>
> In fact as far as I can tell (I'm slightly lost within the Galaxy code at
> this point), it looks like the working directory is created within the job
> wrapper (via the objectstore interface) before the handler is assigned.
>
> I'm wondering if a possible workaround might be to use Pulsar running on the
> same server, but it looks like a lot of overhead for my current problem
> (especially as I don't have any experience currently with using Pulsar).
>
> -- Re cuffdiff cummeRbund SQLite database error:
>
> It looks like changing the job_working_directory to a non-lustre filesystem
> fixes this problem.
>
> Best wishes
>
> Peter
>
>
> On 08/03/16 09:37, Peter Briggs wrote:
>>
>> Hello
>>
>> I've encountered an issue with running the cuffdiff tool on our local
>> production Galaxy instance.
>>
>> Specifically when a cummerbund SQLite database is requested as output
>> then the tool fails with an error:
>>
>> Creating database ./cummeRbund.sqlite
>> Error in sqliteSendQuery(con, statement, bind.data) :
>>error in statement: disk I/O error
>> Error in sqliteSendQuery(con, statement, bind.data) :
>>error in statement: disk I/O error
>> Calls: readCufflinks ... .local -> sqliteGetQuery -> sqliteSendQuery ->
>> .Call
>> Execution halted
>>
>> Our Galaxy is configured to use a LustreFS scratch directory for the
>> 'job_working_directory', which I understand is where each job will have
>> its own working directory created, and I'm wondering if the SQLite error
>> above is a manifestation of a general problem with SQLite on LustreFS
>> (see e.g. the answer to this BioStars question
>> https://www.biostars.org/p/115452/).
>>
>> The obvious workaround is to change 'job_working_directory', preferably
>> just for the cuffdiff tool. Does anyone know if it's possible to do this
>> i.e. set 'job_working_directory' on a per-tool basis?
>>
>> (Also, has anyone else seen this specific problem with
>> cuffdiff/cummerbund/SQLite on their local Galaxy instances?)
>>
>> Thanks for your help - any suggestions greatly appreciated,
>>
>> Best wishes
>>
>> Peter
>>
>
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Re: [galaxy-dev] Scaling tools: data available? (Peter van Heusden)

[Peter van Heusden]

Thanks Damion

We've got the collectl based metric collection stuff working and that dumps
data in the Galaxy DB (which you can pull out using the API).

Thanks,
Peter

On 17 March 2016 at 10:45, Dooley, Damion  wrote:

> If you are looking for a simple python program to log cpu% and memory of
> another executable, then analyze.py might do.  Its in
> https://github.com/Public-Health-Bioinformatics/kipper/tree/master/RDP-test
> -case along with a few scripts that show examples of its use.
>
> Damion
> >>
> >> On 02/21/2016 11:13 PM, Peter van Heusden wrote:
> >>
> >> Hi there
> >>
> >> We're researching the resource (CPU time and memory) requirements for
> >>RNA
> >> STAR at the moment. Specifically, we'd like to build up a database of
> >>input
> >> size to resource usage so that we can use this to feed a dynamic
> >> destination mapper (currently our STAR configuration uses a thumbsuck
> >>for
> >> RAM and CPU requirements that is not optimal but works in many cases).
> >>
> >> Has anyone collected these metrics before? And more generally, is anyone
> >> collecting metrics for a range of bioinformatics tools? A database like
> >> this could be very useful!
> >>
> >> Thanks!
> >> Peter
> >>
>
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Re: [galaxy-dev] planemo update failing on testtoolshed

[Peter van Heusden]

The repo is empty, so there is nothing to delete at this stage. And I can't
figure out how to delete the thing entirely.

I looked at the splitFasta tool, and also the splitfasta tool from rnateam
(in the test toolshed) and these split into 1 file for each sequence as
opposed to a certain number of chunks.

Peter

On 18 March 2016 at 21:11, Björn Grüning  wrote:

> Hi Peter,
>
> can you try to delete files with the web interface?
>
> I saw the tool name, do you know this small tool?
>
> https://github.com/bgruening/galaxytools/blob/master/tools/splitfasta/splitFasta.xml
>
> Cheers,
> Bjoern
>
> Am 18.03.2016 um 20:03 schrieb Peter van Heusden:
> > Hi there
> >
> > I'm trying to update a newly created tool on the test tool shed and I
> > get this error:
> >
> > $ planemo shed_update -t testtoolshed
> > cd '/home/pvh/PycharmProjects/split_fasta_chunks' && git rev-parse HEAD
> > cd '/home/pvh/PycharmProjects/split_fasta_chunks' && git diff --quiet
> > Could not update split_fasta_chunks
> > Unexpected response from galaxy: 500: 
> >   Internal Server Error
> >   
> > Internal Server Error
> > The server has either erred or is incapable of performing
> > the requested operation.
> >
> > 
> > 
> > 
> > WSGI Server
> >   
> > 
> >
> > Repository metadata updated.
> > Failed to update a repository.
> >
> > I might have accidentally created a "bad" repository that is leading to
> > this error. This is with version 0.23.0. Alternately, is there a way to
> > delete the tool so that I can try and recreate it?
> >
> > Thanks!
> > Peter
> >
> >
> > ___
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> >
>
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[galaxy-dev] Using forms to collect user info at registration

[Peter Briggs]

Hello

I'm trying to set up a form within Galaxy to collect some user info at 
registration time. The only documentation I've found on this 
functionality is:


https://wiki.galaxyproject.org/Admin/Config/User%20Information

which seems to be precisely what I need.

However I can't make this work as described. When I set up a form and 
then go to the registration page, instead of the additional form options 
I get a single field called "User type" with a drop-down menu widget 
with a single option ("User registration form" i.e. the name of the form 
that I created).


I've looked to see if there is a config option to turn something on, or 
if I need to create a role, but so far nothing I've tried seems to make 
a difference.


Does anyone have any suggestions on how I might get this feature to 
operate as advertised? (Btw I'm seeing this in both 15.10 and 16.01.)


Thanks for your help,

Best wishes

Peter

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482
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Re: [galaxy-dev] Using forms to collect user info at registration

[Martin Čech]

Hello Peter,

you are right, this seems broken, sorry about that.
I have created an issue to track the resolution of this bug:
https://github.com/galaxyproject/galaxy/issues/1937

Thank you for reporting it.

Martin

On Wed, Mar 16, 2016 at 10:16 AM Peter Briggs 
wrote:

> Hello
>
> I'm trying to set up a form within Galaxy to collect some user info at
> registration time. The only documentation I've found on this
> functionality is:
>
> https://wiki.galaxyproject.org/Admin/Config/User%20Information
>
> which seems to be precisely what I need.
>
> However I can't make this work as described. When I set up a form and
> then go to the registration page, instead of the additional form options
> I get a single field called "User type" with a drop-down menu widget
> with a single option ("User registration form" i.e. the name of the form
> that I created).
>
> I've looked to see if there is a config option to turn something on, or
> if I need to create a role, but so far nothing I've tried seems to make
> a difference.
>
> Does anyone have any suggestions on how I might get this feature to
> operate as advertised? (Btw I'm seeing this in both 15.10 and 16.01.)
>
> Thanks for your help,
>
> Best wishes
>
> Peter
>
> --
> Peter Briggs peter.bri...@manchester.ac.uk
> Bioinformatics Core Facility University of Manchester
> B.1083 Michael Smith Bldg Tel: (0161) 2751482
> ___
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[galaxy-dev] automatic adding of a tab in a fastq header

[Fabien Mareuil]

Hi,

We got a problem with the new version of Data libraries. When we upload 
a fastq file from a User Directory, a tabulation character is added in 
the header in replacement of a space character.


from @HWI-D00395:188:HYGNFADXX:2:1108:1315:1965 1:N:0:ATGAGC to 
@HWI-D00395:188:HYGNFADXX:2:1108:1315:1965  1:N:0:ATGAGC


This behavior causes an error with cutadapt 1.6 (maybe with other tools) 
because it doesn't work with tab character. With the direct upload tool 
or the deprecated version of Data Libraries no tab character is added.Do 
you have some idea to correct this problem? Thanks a lot Best regards --
Fabien Mareuil | Centre d'Informatique pour la Biologie 
fabien.mare...@pasteur.fr  | Institut 
Pasteur 25,28 rue du Docteur Roux 75015 Paris, France
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[galaxy-dev] init scripts version 16.01

[Eric Kuyt]

Hey guys, today I updated to the latest version of galaxy. No I noticed
that because of the new virtualenv/wheel startup procedure, the init
scripts as mentioned here
https://wiki.galaxyproject.org/Events/GCC2012/TrainingDay/WS5?highlight=%28init.d%29

are not working anymore. Whet is the new startup procedure?

Thanks

Eric Kuijt
-- 
Central Veterinary Institute of Wageningen UR (CVI)
Department of Infection Biology
PO box 65, 8200 AB Lelystad, NL
Visiting address: ASG, Edelhertweg 15, 8219 PH Lelystad

Tel:  +31-(0)320-293391
Fax: +31-(0)320-238153
E-mail: eric.ku...@wur.nl
Web: http://www.cvi.wur.nl
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Re: [galaxy-dev] Scaling tools: data available? (Peter van Heusden)

[Dooley, Damion]

If you are looking for a simple python program to log cpu% and memory of
another executable, then analyze.py might do.  Its in
https://github.com/Public-Health-Bioinformatics/kipper/tree/master/RDP-test
-case along with a few scripts that show examples of its use.

Damion
>>
>> On 02/21/2016 11:13 PM, Peter van Heusden wrote:
>>
>> Hi there
>>
>> We're researching the resource (CPU time and memory) requirements for
>>RNA
>> STAR at the moment. Specifically, we'd like to build up a database of
>>input
>> size to resource usage so that we can use this to feed a dynamic
>> destination mapper (currently our STAR configuration uses a thumbsuck
>>for
>> RAM and CPU requirements that is not optimal but works in many cases).
>>
>> Has anyone collected these metrics before? And more generally, is anyone
>> collecting metrics for a range of bioinformatics tools? A database like
>> this could be very useful!
>>
>> Thanks!
>> Peter
>>

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