Hi Peter,

FYI: just found on the galaxy documentation a paragraph that even recommends running upload on the cluster:

https://galaxyproject.org/admin/config/performance/cluster/

"""
If your cluster nodes have Internet access (NAT is okay) and you want to run the data source tools (upload, ucsc, etc.) on the cluster (doing so is highly recommended), set new_file_path in galaxy.ini to a directory somewhere in your shared filesystem:
"""

Cheers,
Matthias


On 10.07.2017 11:11, Matthias Bernt wrote:
Dear Peter,

my job_conf.xml is attached.


Best,
Matthuas

On 08.07.2017 18:00, galaxy-dev-requ...@lists.galaxyproject.org wrote:
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Today's Topics:

    1. Re: any introduce for how Mako and JavaScript work in    galaxy?
       (Daniel Blankenberg)
    2. Re: ustacks - bad interpreter (Björn Grüning)
    3. Re: Improved DRMAAJobRunner (Peter van Heusden) (Matthias Bernt)
    4. Re: Improved DRMAAJobRunner (Peter van Heusden)
       (Peter van Heusden)


----------------------------------------------------------------------

Message: 1
Date: Thu, 6 Jul 2017 22:36:27 -0400
From: Daniel Blankenberg <dan.blankenb...@gmail.com>
To: Steven Shen <ishenwei...@gmail.com>
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] any introduce for how Mako and JavaScript
    work in    galaxy?
Message-ID:
    <CAE9nRFg+Edj2=3+K=6+FZCxj5=hb4togw+lm++e+sd1+j2+...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

Hi Steven,

For a quick first pass, have you taken a look at https://github.com/
galaxyproject/galaxy/blob/dev/client/README.md?


Thanks for using Galaxy,

Dan

On Thu, Jul 6, 2017 at 10:11 PM, Steven Shen <ishenwei...@gmail.com> wrote:

Hi everyone,

I want to make some change for my local galaxy web, actually I can edit
galaxy_path/static/scripts/bundled/*.js directly.

It seems mako templates are used for galaxy, as well as many JavaScript
files, but I don't know how they work. So is there any introduce for how
mako and JavaScript files working in galaxy?

Thank you very much.

Steven

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Message: 2
Date: Sat, 8 Jul 2017 11:31:31 +0200
From: Björn Grüning <bjoern.gruen...@gmail.com>
To: David Meltzer <david.melt...@glasgow.ac.uk>, Nate Coraor
    <n...@bx.psu.edu>
Cc: "galaxy-dev@lists.galaxyproject.org"
    <galaxy-dev@lists.galaxyproject.org>
Subject: Re: [galaxy-dev] ustacks - bad interpreter
Message-ID: <a5a7d281-6040-f65e-e674-6cb2e9343...@gmail.com>
Content-Type: text/plain; charset=utf-8

Hi,

please also make sure you have a recent conda version. This 80 character
length smalls a lot like an old conda restriction.

Cheers,
Bjoern

Am 07.07.2017 um 18:09 schrieb David Meltzer:
Good afternoon,


Thank you for that! I will look in to it!


Best Regards,

David Jacob Meltzer


*From: *Nate Coraor <n...@bx.psu.edu>
*Date: *Friday, July 7, 2017 at 5:02 PM
*To: *David Meltzer <david.melt...@glasgow.ac.uk>
*Cc: *Yvan Le Bras <yvan.le-b...@mnhn.fr>,
"galaxy-dev@lists.galaxyproject.org" <galaxy-dev@lists.galaxyproject.org>
*Subject: *Re: [galaxy-dev] ustacks - bad interpreter


Hi David,


You may want to have a look at the first line of:


/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a13db6458b9361ca87c93be9feed656f9938ebcc435642f3a0a3/bin/stacks_summary.py


The shell is claiming it is:


#!/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a1


When it should be:


#!/home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a13db6458b9361ca87c93be9feed656f9938ebcc435642f3a0a3/bin/python


However, it could be that the line is correct and the output was
truncated, or the shell has a length limit for the shebang (although the
truncated string is only 79 characters, I'd be surprised if the limit
for your shell was that short).


--nate


On Fri, Jul 7, 2017 at 8:21 AM, David Meltzer
<david.melt...@glasgow.ac.uk <mailto:david.melt...@glasgow.ac.uk>> wrote:

     Good afternoon,


     I will do my best!


     Best Regards,
     David


     *From: *Yvan Le Bras <yvan.le-b...@mnhn.fr
     <mailto:yvan.le-b...@mnhn.fr>>
     *Date: *Friday, July 7, 2017 at 1:06 PM


     *To: *David Meltzer <david.melt...@glasgow.ac.uk
     <mailto:david.melt...@glasgow.ac.uk>>,
     "galaxy-dev@lists.galaxyproject.org
     <mailto:galaxy-dev@lists.galaxyproject.org>"
     <galaxy-dev@lists.galaxyproject.org
     <mailto:galaxy-dev@lists.galaxyproject.org>>
     *Subject: *RE : [galaxy-dev] ustacks - bad interpreter


     No problem, I was not writing my question clearly...


     I suspect a pb with the stacks_summary related script... Can you
     investigate it, I unfortunately can't work on it for now. .. Maybe
     ""just"" a missing python interpreter invocation somewhere. .. when
     executing stacks_summary. ...



     -------- Message d'origine --------
     De : David Meltzer <david.melt...@glasgow.ac.uk
     <mailto:david.melt...@glasgow.ac.uk>>
     Date : 07/07/2017 13:47 (GMT+01:00)
     À : Yvan Le Bras <yvan.le-b...@mnhn.fr
     <mailto:yvan.le-b...@mnhn.fr>>, galaxy-dev@lists.galaxyproject.org
     <mailto:galaxy-dev@lists.galaxyproject.org>
     Objet : Re: [galaxy-dev] ustacks - bad interpreter


     Good afternoon,


     I apologize. I misunderstood the question. Yes, stacks_summary has
     been installed correctly as have stacks and velvet.


     Additionally, the tool is outputting three items into the history -


     Summary from Stacks – red (error)

     Ustacks.log – red (error)

     Stacks from Data – green (successful)


     Best Regards,

     David Jacob Meltzer


     *From: *galaxy-dev <galaxy-dev-boun...@lists.galaxyproject.org
     <mailto:galaxy-dev-boun...@lists.galaxyproject.org>> on behalf of
     David Meltzer <david.melt...@glasgow.ac.uk
     <mailto:david.melt...@glasgow.ac.uk>>
     *Date: *Friday, July 7, 2017 at 12:31 PM
     *To: *Yvan Le Bras <yvan.le-b...@mnhn.fr
     <mailto:yvan.le-b...@mnhn.fr>>, "galaxy-dev@lists.galaxyproject.org
     <mailto:galaxy-dev@lists.galaxyproject.org>"
     <galaxy-dev@lists.galaxyproject.org
     <mailto:galaxy-dev@lists.galaxyproject.org>>
     *Subject: *Re: [galaxy-dev] ustacks - bad interpreter


     Good afternoon,


I am sorry. I don’t see a tool called stacks_summary installed on my
     system or available on the toolshed.


     Best Regards,

     David


     *From: *Yvan Le Bras <yvan.le-b...@mnhn.fr
     <mailto:yvan.le-b...@mnhn.fr>>
     *Date: *Friday, July 7, 2017 at 12:08 PM
     *To: *David Meltzer <david.melt...@glasgow.ac.uk
     <mailto:david.melt...@glasgow.ac.uk>>,
     "galaxy-dev@lists.galaxyproject.org
     <mailto:galaxy-dev@lists.galaxyproject.org>"
     <galaxy-dev@lists.galaxyproject.org
     <mailto:galaxy-dev@lists.galaxyproject.org>>
     *Subject: *RE : [galaxy-dev] ustacks - bad interpreter


     Hi David,


     A pb with stacks_summary apparently... and ustacks is working well
apparently... Can you check you have stacks_summary well installed ?
     I think it is but there is a pb using it...


     Cheers,


     Yvan




     Envoyé depuis mon appareil Samsung



     -------- Message d'origine --------
     De : David Meltzer <david.melt...@glasgow.ac.uk
     <mailto:david.melt...@glasgow.ac.uk>>
     Date : 07/07/2017 12:38 (GMT+01:00)
     À : galaxy-dev@lists.galaxyproject.org
     <mailto:galaxy-dev@lists.galaxyproject.org>
     Objet : [galaxy-dev] ustacks - bad interpreter


     Good morning,


     I have a user attempting to run ustacks. They are receiving the
     following error


     Fatal error: Exit code 126 (Error in Stacks execution)

/home/big_galaxy/galaxy/database/jobs_directory/079/79363/tool_script.sh: /home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a13db6458b9361ca87c93be9feed656f9938ebcc435642f3a0a3/bin/stacks_summary.py: /home/big_galaxy/galaxy/tool_dependencies/_conda/envs/mulled-v1-8e6d35eac718a1:
     bad interpreter: No such file or directory


     The tool produces an additional output on the bug report –


     ustacks parameters selected:

       Sample ID: 1

       Min depth of coverage to create a stack: 3

       Max distance allowed between stacks: 2

       Max distance allowed to align secondary reads: 4

       Max number of stacks allowed per de novo locus: 3

       Deleveraging algorithm: disabled

       Removal algorithm: enabled

       Model type: SNP

       Alpha significance level for model: 0.05

       Gapped alignments: disabled

     Parsing stacks_inputs/ZU-6.fq

     Loading RAD-Tags...done

     Loaded 933120 RAD-Tags.

       Inserted 256463 elements into the RAD-Tags hash map.

       0 reads contained uncalled nucleotides that were modified.

65509 initial stacks were populated; 190954 stacks were set aside as
     secondary reads.

     Initial coverage mean: 10.9276; Std Dev: 25.3864; Max: 4650

     Deleveraging trigger: 36; Removal trigger: 62

     Calculating distance for removing repetitive stacks.

       Distance allowed between stacks: 1; searching with a k-mer length
     of 35 (36 k-mers per read); 1 k-mer hits required.

     Removing repetitive stacks.

       Removed 993 stacks.

       64677 stacks remain for merging.

Post-Repeat Removal, coverage depth Mean: 10.2655; Std Dev: 9.03472;
     Max: 62

     Calculating distance between stacks...

       Distance allowed between stacks: 2; searching with a k-mer length
     of 23 (48 k-mers per read); 2 k-mer hits required.

     Merging stacks, maximum allowed distance: 2 nucleotide(s)

       64677 stacks merged into 57327 loci; deleveraged 0 loci;
     blacklisted 189 loci.

After merging, coverage depth Mean: 11.0747; Std Dev: 9.82823; Max: 91

     Merging remainder radtags

       217265 remainder sequences left to merge.

       Distance allowed between stacks: 4; searching with a k-mer length
     of 13 (58 k-mers per read); 6 k-mer hits required.

Matched 26211 remainder reads; unable to match 191054 remainder reads.

     After remainders merged, coverage depth Mean: 11.5347; Std Dev:
     9.95581; Max: 93

     Calling final consensus sequences, invoking SNP-calling model...

     Number of utilized reads: 742066

     Writing loci, SNPs, and alleles to 'stacks_outputs/'...

       Refetching sequencing IDs from stacks_inputs/ZU-6.fq... read
     933120 sequence IDs.

     done.

     ustacks is done.


     I am not sure what is causing the bad interpreter: No such file or
     directory. The tools are correctly installed along with its
     requisite conda packages.


     Any help would be greatly appreciated.


     Best Regards,


     David


     ___________________________________________________________
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------------------------------

Message: 3
Date: Sat, 08 Jul 2017 11:56:50 +0200
From: Matthias Bernt <m.be...@ufz.de>
To: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Improved DRMAAJobRunner (Peter van Heusden)
Message-ID: <fb33e9595421.5960c...@ufz.de>
Content-Type: text/plain; charset="utf-8"

Hi Peter,

Code looks interesting. This is for Univa Grid Engine?

In its current state its tailored for the Univa Grid Engine. But the drmaa library code that is based on job_info() and wait() should run on all grid engines. For the command line based code changes might be necessary for the different grid engines. (Currently there is only a small bug, because wait() is currently called twice for finished jobs: in the repeated polling and then in the final check. The second call won't work which causes a fallback to qacct. I will fix this
soon.)
I guess that the output of qstat and qacct will be different. But I think this can be configured one just needs a way to get the info which grid engine is running.

In terms of the upload jobs, are those not designed to be run as 'local' jobs and not with the 'real user' setting?

Sounds reasonable, but this is not what is happening on my installation of galaxy. Any idea where I could start to find the problem.

Best,
Matthias
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Message: 4
Date: Sat, 08 Jul 2017 13:52:39 +0000
From: Peter van Heusden <p...@sanbi.ac.za>
To: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Improved DRMAAJobRunner (Peter van Heusden)
Message-ID:
    <cak1rexg1w4vkvvwamdapsevgq93xscn1ipf8t8ibjytytpr...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

On Sat, 8 Jul 2017 at 11:56 Matthias Bernt <m.be...@ufz.de> wrote:

Hi Peter,

Code looks interesting. This is for Univa Grid Engine?

In its current state its tailored for the Univa Grid Engine. But the drmaa library code that is based on job_info() and wait() should run on all grid
engines.
For the command line based code changes might be necessary for the
different grid engines. (Currently there is only a small bug, because
wait() is currently
called twice for finished jobs: in the repeated polling and then in the
final check. The second call won't work which causes a fallback to qacct. I
will fix this
soon.)
I guess that the output of qstat and qacct will be different. But I think
this can be configured one just needs a way to get the info which grid
engine is running.

In terms of the upload jobs, are those not designed to be run as 'local'
jobs and not with the 'real user' setting?

Sounds reasonable, but this is not what is happening on my installation of
galaxy. Any idea where I could start to find the problem.

I'm not an expert on this, but what does your job_conf.xml look like?

Peter

Best,
Matthias ___________________________________________________________
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