date:20190522

[galaxy-dev] Re: samtools_slice_bam/2.0.1 no options available

2019-05-22 Thread Martin Čech

Eric: I recommend https://help.galaxyproject.org/ for your question, it
might reach a better audience there.

Paula: I believe you can unsubscribe here:
https://lists.galaxyproject.org/lists/galaxy-dev.lists.galaxyproject.org/

Regards,

Martin

On Wed, May 22, 2019 at 12:49 PM Paula Berrutti 
wrote:

> Please,
>
> Remove my email fro the list
>
> Thank you,
>
> Paula
>
> Obter o Outlook para Android
>
> 
> From: Eric Kuyt 
> Sent: Wednesday, May 22, 2019 9:33:57 AM
> To: galaxy-dev@lists.galaxyproject.org
> Subject: [galaxy-dev] Re: samtools_slice_bam/2.0.1 no options available
>
> Is this the right spot for this question? Or is it better to ask elsewhere?
>
> On Mon, 13 May 2019 at 09:50, Eric Kuyt  wrote:
>
> > Hey all,
> >
> > I have a question about the samtools_slice_bam tool in the samtools
> suite.
> >
> > It seems the references variable remains empty after re-detecting
> > metadata. I now tried sorting the bam in galaxy and manually in samtools,
> > but no references coming up.
> >
> > I also ran a breakpoint in the binary.Bam.set_meta but it doesn't seem to
> > be catched.
> >
> > Any ideas? Thx.
> >
> > Eric
> >
> >
> >
> >
> >
> ___
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[galaxy-dev] Re: new datasets appear in database/files/000/

2019-05-22 Thread Dannon Baker

Hi Jochen,

Yes, those new directories would coincide with when you passed 100,000
datasets on your instance, so congrats!  You can see the code that builds
this hashed path here:
https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/util/__init__.py#L137

So, for example, dataset id `9` Will be in folder 'datasets/099/'.
Dataset '10' will be in 'datasets/000/100/'.

Sorry for the slow response, hope this clears up the storage path logic!

-Dannon

On Tue, May 21, 2019 at 11:38 AM Jochen Bick 
wrote:

> Coming back to my question:
>
> this is how an ls -ls looks in my database folder...
>
> 2. Apr 14:40 000/
> 9. Nov 2015 005/
> 19. Nov 2018 007/
> 19. Nov 2018 008/
> 3. Dez 2015 010/
> 10. Jan 2017 012/
> 10. Jan 2017 013/
> 29. Jun 2017 014/
> 4. Jul 2017 015/
> 9. Jan 2018 018/
> 29. Jun 2017 020/
> 21. Sep 2016 021/
> 20. Mär 2018 032/
> 29. Jan 09:38 033/
> 29. Jan 10:32 034/
> 16. Jul 2018 035/
> 30. Okt 2018 036/
> 30. Okt 2018 037/
> 30. Okt 2018 038/
> 30. Okt 2018 039/
> 29. Aug 2018 070/
> 29. Aug 2018 071/
> 29. Aug 2018 072/
> 29. Aug 2018 073/
> 29. Aug 2018 074/
> 29. Aug 2018 075/
> 29. Aug 2018 076/
> 29. Aug 2018 077/
> 29. Aug 2018 078/
> 29. Aug 2018 079/
> 29. Aug 2018 080/
> 29. Aug 2018 081/
> 29. Aug 2018 082/
> 29. Aug 2018 083/
> 29. Aug 2018 084/
> 29. Aug 2018 085/
> 29. Aug 2018 086/
> 29. Aug 2018 087/
> 29. Aug 2018 088/
> 29. Aug 2018 089/
> 29. Aug 2018 090/
> 29. Aug 2018 091/
> 29. Aug 2018 092/
> 29. Aug 2018 093/
> 29. Aug 2018 094/
> 29. Aug 2018 095/
> 31. Aug 2018 096/
> 30. Aug 2018 097/
> 1. Sep 2018 098/
> 24. Okt 2018 099/
>
>
> if you look into the 000 folder it restarts:
>
> 10. Dez 19:36 100/
> 30. Nov 10:45 101/
> 10. Dez 19:39 102/
> 10. Dez 19:37 103/
> 11. Jan 15:13 104/
> 11. Jan 11:31 105/
> 22. Jan 14:33 106/
> 8. Feb 10:46 107/
> 14. Feb 15:47 108/
> 21. Mär 11:00 109/
> 2. Apr 15:22 110/
> 21. Mai 17:17 111/
>
> is this the expected behavior?
>
> The only thing we did was we archived some of the very early generated
> datasets. Is this maybe the problem?
>
>
> Cheers Jochen
>
>
> On 14.05.19 15:32, Jochen Bick wrote:
> > Hi,
> >
> > today we found out that some of our files in your galaxy instance are
> > new in "database/files/000/" which is the first folder of your database
> > files. Could some please explain me how galaxy generates new file names?
> > and how this is possible?
> >
> > Thanks in advance Jochen
> >
> --
> ETH Zurich
> *Jochen Bick*
> Animal Physiology
> Institute of Agricultural Sciences
> Postal address: Universitätstrasse 2 / LFW B 58.1
> 8092 Zurich, Switzerland
> Office: Eschikon 27
> 8315 Lindau, Switzerland
>
> Phone +41 52 354 92 06
> jochen.b...@usys.ethz.ch 
> www.ap.ethz.ch
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   %(web_page_url)s
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/
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[galaxy-dev] Re: galaxy-dev Digest, Vol 155, Issue 3

2019-05-22 Thread Jochen Bick

Thanks Matthias. Good to know. I thought we might confused the system by 
archiving a part of the data.

Cheers Jochen

⁣Get BlueMail for Android 

On May 22, 2019, 08:42, at 08:42, Matthias Bernt  wrote:
>Dear Jochen,
>
>I don't know if its excpected. But at least I can tell that the same is
>
>happening here. And I can add if the 000 folder contains 000-999 the 
>pattern repeats in 001.
>
>Cheers,
>Matthias
>
>On 21.05.19 17:38, galaxy-dev-requ...@lists.galaxyproject.org wrote:
>> Coming back to my question:
>> 
>> this is how an ls -ls looks in my database folder...
>> 
>> 2. Apr 14:40 000/
>> 9. Nov 2015 005/
>> 19. Nov 2018 007/
>> 19. Nov 2018 008/
>> 3. Dez 2015 010/
>> 10. Jan 2017 012/
>> 10. Jan 2017 013/
>> 29. Jun 2017 014/
>> 4. Jul 2017 015/
>> 9. Jan 2018 018/
>> 29. Jun 2017 020/
>> 21. Sep 2016 021/
>> 20. Mär 2018 032/
>> 29. Jan 09:38 033/
>> 29. Jan 10:32 034/
>> 16. Jul 2018 035/
>> 30. Okt 2018 036/
>> 30. Okt 2018 037/
>> 30. Okt 2018 038/
>> 30. Okt 2018 039/
>> 29. Aug 2018 070/
>> 29. Aug 2018 071/
>> 29. Aug 2018 072/
>> 29. Aug 2018 073/
>> 29. Aug 2018 074/
>> 29. Aug 2018 075/
>> 29. Aug 2018 076/
>> 29. Aug 2018 077/
>> 29. Aug 2018 078/
>> 29. Aug 2018 079/
>> 29. Aug 2018 080/
>> 29. Aug 2018 081/
>> 29. Aug 2018 082/
>> 29. Aug 2018 083/
>> 29. Aug 2018 084/
>> 29. Aug 2018 085/
>> 29. Aug 2018 086/
>> 29. Aug 2018 087/
>> 29. Aug 2018 088/
>> 29. Aug 2018 089/
>> 29. Aug 2018 090/
>> 29. Aug 2018 091/
>> 29. Aug 2018 092/
>> 29. Aug 2018 093/
>> 29. Aug 2018 094/
>> 29. Aug 2018 095/
>> 31. Aug 2018 096/
>> 30. Aug 2018 097/
>> 1. Sep 2018 098/
>> 24. Okt 2018 099/
>> 
>> 
>> if you look into the 000 folder it restarts:
>> 
>> 10. Dez 19:36 100/
>> 30. Nov 10:45 101/
>> 10. Dez 19:39 102/
>> 10. Dez 19:37 103/
>> 11. Jan 15:13 104/
>> 11. Jan 11:31 105/
>> 22. Jan 14:33 106/
>> 8. Feb 10:46 107/
>> 14. Feb 15:47 108/
>> 21. Mär 11:00 109/
>> 2. Apr 15:22 110/
>> 21. Mai 17:17 111/
>> 
>> is this the expected behavior?
>> 
>> The only thing we did was we archived some of the very early
>generated
>> datasets. Is this maybe the problem?
>> 
>> 
>> Cheers Jochen
>> 
>> 
>> On 14.05.19 15:32, Jochen Bick wrote:
>>> Hi,
>>>
>>> today we found out that some of our files in your galaxy instance
>are
>>> new in "database/files/000/" which is the first folder of your
>database
>>> files. Could some please explain me how galaxy generates new file
>names?
>>> and how this is possible?
>>>
>>> Thanks in advance Jochen
>>>
>> -- ETH Zurich *Jochen Bick* Animal Physiology Institute of
>Agricultural 
>> Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 8092
>Zurich, 
>> Switzerland Office: Eschikon 27 8315 Lindau, Switzerland Phone +41 52
>
>> 354 92 06 jochen.b...@usys.ethz.ch  
>> www.ap.ethz.ch
>
>-- 
>
>---
>Matthias Bernt
>Bioinformatics Service
>Molekulare Systembiologie (MOLSYB)
>Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
>Helmholtz Centre for Environmental Research GmbH - UFZ
>Permoserstraße 15, 04318 Leipzig, Germany
>Phone +49 341 235 482296,
>m.be...@ufz.de, www.ufz.de
>
>Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
>Helmholtz Centre for Environmental Research GmbH - UFZ 
>Permoserstraße 15, 04318 Leipzig, Germany
>Phone +49 341 235 1269, Fax +49 341 235 1468 (optional)
>max.musterm...@ufz.de, www.ufz.de
>
>Sitz der Gesellschaft/Registered Office: Leipzig
>Registergericht/Registration Office: Amtsgericht Leipzig
>Handelsregister Nr./Trade Register Nr.: B 4703
>Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: 
>MinDirig Wilfried Kraus
>Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
>Prof. Dr. Georg Teutsch
>Administrative Geschäftsführerin/Administrative Managing Director:
>Dr. Sabine König
___
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[galaxy-dev] Re: galaxy-dev Digest, Vol 155, Issue 3

2019-05-22 Thread Matthias Bernt


Dear Jochen,

I don't know if its excpected. But at least I can tell that the same is 
happening here. And I can add if the 000 folder contains 000-999 the 
pattern repeats in 001.


Cheers,
Matthias

On 21.05.19 17:38, galaxy-dev-requ...@lists.galaxyproject.org wrote:

Coming back to my question:

this is how an ls -ls looks in my database folder...

2. Apr 14:40 000/
9. Nov 2015 005/
19. Nov 2018 007/
19. Nov 2018 008/
3. Dez 2015 010/
10. Jan 2017 012/
10. Jan 2017 013/
29. Jun 2017 014/
4. Jul 2017 015/
9. Jan 2018 018/
29. Jun 2017 020/
21. Sep 2016 021/
20. Mär 2018 032/
29. Jan 09:38 033/
29. Jan 10:32 034/
16. Jul 2018 035/
30. Okt 2018 036/
30. Okt 2018 037/
30. Okt 2018 038/
30. Okt 2018 039/
29. Aug 2018 070/
29. Aug 2018 071/
29. Aug 2018 072/
29. Aug 2018 073/
29. Aug 2018 074/
29. Aug 2018 075/
29. Aug 2018 076/
29. Aug 2018 077/
29. Aug 2018 078/
29. Aug 2018 079/
29. Aug 2018 080/
29. Aug 2018 081/
29. Aug 2018 082/
29. Aug 2018 083/
29. Aug 2018 084/
29. Aug 2018 085/
29. Aug 2018 086/
29. Aug 2018 087/
29. Aug 2018 088/
29. Aug 2018 089/
29. Aug 2018 090/
29. Aug 2018 091/
29. Aug 2018 092/
29. Aug 2018 093/
29. Aug 2018 094/
29. Aug 2018 095/
31. Aug 2018 096/
30. Aug 2018 097/
1. Sep 2018 098/
24. Okt 2018 099/


if you look into the 000 folder it restarts:

10. Dez 19:36 100/
30. Nov 10:45 101/
10. Dez 19:39 102/
10. Dez 19:37 103/
11. Jan 15:13 104/
11. Jan 11:31 105/
22. Jan 14:33 106/
8. Feb 10:46 107/
14. Feb 15:47 108/
21. Mär 11:00 109/
2. Apr 15:22 110/
21. Mai 17:17 111/

is this the expected behavior?

The only thing we did was we archived some of the very early generated
datasets. Is this maybe the problem?


Cheers Jochen


On 14.05.19 15:32, Jochen Bick wrote:

Hi,

today we found out that some of our files in your galaxy instance are
new in "database/files/000/" which is the first folder of your database
files. Could some please explain me how galaxy generates new file names?
and how this is possible?

Thanks in advance Jochen

-- ETH Zurich *Jochen Bick* Animal Physiology Institute of Agricultural 
Sciences Postal address: Universitätstrasse 2 / LFW B 58.1 8092 Zurich, 
Switzerland Office: Eschikon 27 8315 Lindau, Switzerland Phone +41 52 
354 92 06 jochen.b...@usys.ethz.ch  
www.ap.ethz.ch


--

---
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
m.be...@ufz.de, www.ufz.de

Helmholtz-Zentrum für Umweltforschung GmbH - UFZ
Helmholtz Centre for Environmental Research GmbH - UFZ  
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 1269, Fax +49 341 235 1468 (optional)
max.musterm...@ufz.de, www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: 
MinDirig Wilfried Kraus

Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Georg Teutsch
Administrative Geschäftsführerin/Administrative Managing Director:
Dr. Sabine König
___
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[galaxy-dev] Re: samtools_slice_bam/2.0.1 no options available

2019-05-22 Thread Paula Berrutti

Please,

Remove my email fro the list

Thank you,

Paula

Obter o Outlook para Android

From: Eric Kuyt 
Sent: Wednesday, May 22, 2019 9:33:57 AM
To: galaxy-dev@lists.galaxyproject.org
Subject: [galaxy-dev] Re: samtools_slice_bam/2.0.1 no options available

Is this the right spot for this question? Or is it better to ask elsewhere?

On Mon, 13 May 2019 at 09:50, Eric Kuyt  wrote:

> Hey all,
>
> I have a question about the samtools_slice_bam tool in the samtools suite.
>
> It seems the references variable remains empty after re-detecting
> metadata. I now tried sorting the bam in galaxy and manually in samtools,
> but no references coming up.
>
> I also ran a breakpoint in the binary.Bam.set_meta but it doesn't seem to
> be catched.
>
> Any ideas? Thx.
>
> Eric
>
>
>
>
>
___
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[galaxy-dev] Workflow assigning columns on output causes "Uncaught exception in exposed API method"

2019-05-22 Thread Peter Briggs

Dear Devs

We've encountered a problem trying to run a workflow on our local Galaxy 
instance, which is resulting in an "uncaught exception in exposed API method" 
message displayed in the Galaxy window.

The most trivial workflow exhibiting the problem consists of a single 'cut' 
task, where the output of the task is configured to change the datatype to 
"interval", and to explicitly assign the chrom, start and end columns to 1,2 
and 3. Attempts to run this workflow generate the API exception.

If the workflow is updated so that the column assignments are no longer 
attempted then the workflow is able to start without apparent problems.

Our local Galaxy instance is a bit out of data (18.09) but I have been able to 
reproduce this error on Galaxy main so it looks like it also affects later 
versions. The failing workflow can be accessed on main via:

https://usegalaxy.org/u/pjbriggs/w/cut-workflow-reassign-columns-fails-with-uncaught-api-exception

The same workflow with the column assignment removed is accessible via:

https://usegalaxy.org/u/pjbriggs/w/cut-workflow-no-column-reassignment

(Main offers two variants of the 'cut' tool - as far as I can tell this problem 
happens with both.)

Apologies if this has already been reported elsewhere - any suggestions for a 
workaround appreciated.

Thanks,

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] Re: samtools_slice_bam/2.0.1 no options available

2019-05-22 Thread Eric Kuyt

Is this the right spot for this question? Or is it better to ask elsewhere?

On Mon, 13 May 2019 at 09:50, Eric Kuyt  wrote:

> Hey all,
>
> I have a question about the samtools_slice_bam tool in the samtools suite.
>
> It seems the references variable remains empty after re-detecting
> metadata. I now tried sorting the bam in galaxy and manually in samtools,
> but no references coming up.
>
> I also ran a breakpoint in the binary.Bam.set_meta but it doesn't seem to
> be catched.
>
> Any ideas? Thx.
>
> Eric
>
>
>
>
>
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  %(web_page_url)s

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

[galaxy-dev] Re: samtools_slice_bam/2.0.1 no options available

[galaxy-dev] Re: new datasets appear in database/files/000/

[galaxy-dev] Re: galaxy-dev Digest, Vol 155, Issue 3

[galaxy-dev] Re: galaxy-dev Digest, Vol 155, Issue 3

[galaxy-dev] Re: samtools_slice_bam/2.0.1 no options available

[galaxy-dev] Workflow assigning columns on output causes "Uncaught exception in exposed API method"

[galaxy-dev] Re: samtools_slice_bam/2.0.1 no options available

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