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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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___________________________________________________________
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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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