Re: [galaxy-dev] Expose Command Line in Galaxy

[Matthias Enders]

Dear Peter,



up to our galaxy admin, we make use of the  Data Manager, so this seems not to 
be the issue here?:



[cid:image001.jpg@01D41868.AAB17910]





Mit freundlichen Grüßen



Matthias Enders

---





GERMAN SEED ALLIANCE GmbH

c/o Norddeutsche Pflanzenzucht

Hans-Georg Lembke KG

Hohenlieth, 24363 Holtsee

Tel.: +49 (0)4351/ 736-189

Fax: + 49 (0)4351/ 736-271

Mobil: +49 (0)151/ 14247360



Email: m.end...@german-seed-alliance.de



Firmensitz Köln

Amtsgericht Köln, HRB 73844



-Ursprüngliche Nachricht-
Von: Peter Cock 
Gesendet: Dienstag, 10. Juli 2018 13:27
An: Matthias Enders 
Cc: Björn Grüning ; 
galaxy-dev@lists.galaxyproject.org
Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy
Priorität: Hoch



Thanks for getting back to us - this was actually my guess from the original 
email - that it was not a blastn error message, but a Galaxy message before 
ever calling BLAST.



My guess is you are seeing this issue, or something like it, with having to 
restart Galaxy to reload the *.loc files?



https://github.com/galaxyproject/galaxy/issues/3171



Peter



On Tue, Jul 10, 2018 at 12:22 PM, Matthias Enders 
mailto:m.end...@german-seed-alliance.de>> 
wrote:

> Dear all,

>

> finally a restart of the container solved the issue with the database/blast.

>

> Regarding the problem with the command line:

> For other tools, the command line showed up, but not for blastn, as the 
> wrapper encountered the error before creating the command line (this is my 
> interpretation).

>

> So the error: "An invalid option was selected for database, 
> 'myCoolDatabaseName', please verify." Was produced by the wrapper, which did 
> not find the new database before restarting the galaxy container.

>

> So the real issue here is perhaps more on "How could blast+ be made aware of 
> new integrated databases, without restarting"?

>

> Mit freundlichen Grüßen

>

> Matthias Enders
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[galaxy-dev] AMD EPYC and Galaxy

[Van Wageningen, GERHARD [gerha...@sun.ac.za]]

Hi All - Just a quick ask - anyone have anything BAD to say about running 
Galaxy on a CENTOS 7.4/Scientific Linux with AMD EPYC chipset?


Its a bit new ... but looks good on paper and we would like to grow the Galaxy 
environment here.


Thanks


Gerhard

Stellenbosch IT


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Disclaimer
Die integriteit en vertroulikheid van hierdie e-pos word deur die volgende 
bepalings gereël. Vrywaringsklousule
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Re: [galaxy-dev] Expose Command Line in Galaxy

[Peter Cock]

Thanks for getting back to us - this was actually my guess from the
original email - that it was not a blastn error message, but a Galaxy
message before ever calling BLAST.

My guess is you are seeing this issue, or something like it, with
having to restart Galaxy to reload the *.loc files?

https://github.com/galaxyproject/galaxy/issues/3171

Peter

On Tue, Jul 10, 2018 at 12:22 PM, Matthias Enders
 wrote:
> Dear all,
>
> finally a restart of the container solved the issue with the database/blast.
>
> Regarding the problem with the command line:
> For other tools, the command line showed up, but not for blastn, as the 
> wrapper encountered the error before creating the command line (this is my 
> interpretation).
>
> So the error: "An invalid option was selected for database, 
> 'myCoolDatabaseName', please verify." Was produced by the wrapper, which did 
> not find the new database before restarting the galaxy container.
>
> So the real issue here is perhaps more on "How could blast+ be made aware of 
> new integrated databases, without restarting"?
>
> Mit freundlichen Grüßen
>
> Matthias Enders
___
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Re: [galaxy-dev] Expose Command Line in Galaxy

[Matthias Enders]

Dear all,

finally a restart of the container solved the issue with the database/blast.

Regarding the problem with the command line:
For other tools, the command line showed up, but not for blastn, as the wrapper 
encountered the error before creating the command line (this is my 
interpretation).

So the error: "An invalid option was selected for database, 
'myCoolDatabaseName', please verify." Was produced by the wrapper, which did 
not find the new database before restarting the galaxy container. 

So the real issue here is perhaps more on "How could blast+ be made aware of 
new integrated databases, without restarting"?

Mit freundlichen Grüßen

Matthias Enders
---


GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht 
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360

Email: m.end...@german-seed-alliance.de

Firmensitz Köln
Amtsgericht Köln, HRB 73844

-Ursprüngliche Nachricht-
Von: Peter Cock  
Gesendet: Dienstag, 10. Juli 2018 12:11
An: Matthias Enders 
Cc: Björn Grüning ; 
galaxy-dev@lists.galaxyproject.org
Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy

There is a setting to enable showing the command line string and full paths on 
disk via the "i" icon from a history entry, see

https://docs.galaxyproject.org/en/master/admin/options.html#expose-dataset-path

# This option allows users to see the full path of datasets via the # "View 
Details" option in the history. This option also exposes the # command line to 
non-administrative users. Administrators can always # see dataset paths.
#expose_dataset_path: false

https://github.com/galaxyproject/galaxy/blob/release_18.05/config/galaxy.yml.sample#L1495

It existed in galaxy.ini too, which has since be replaced by galaxy.yml

Peter

On Tue, Jul 10, 2018 at 8:19 AM, Matthias Enders 
 wrote:
> Dear Björn,
>
> thanks for the very fast reply. Unfortunately, this part is not visible in 
> our instance. (see screenshot). As you can see in the topmost bar, this is 
> done, while being loged in as admin.
>
> Mit freundlichen Grüßen
>
> Matthias Enders
> --
> -
>
>
> GERMAN SEED ALLIANCE GmbH
> c/o Norddeutsche Pflanzenzucht
> Hans-Georg Lembke KG
> Hohenlieth, 24363 Holtsee
> Tel.: +49 (0)4351/ 736-189
> Fax: + 49 (0)4351/ 736-271
> Mobil: +49 (0)151/ 14247360
>
> Email: m.end...@german-seed-alliance.de
>
> Firmensitz Köln
> Amtsgericht Köln, HRB 73844
>
> -Ursprüngliche Nachricht-
> Von: Björn Grüning 
> Gesendet: Dienstag, 10. Juli 2018 09:15
> An: Matthias Enders ; 
> galaxy-dev@lists.galaxyproject.org
> Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy
> Priorität: Hoch
>
> Hi Matthias,
>
> please have a look at the attached screenshot. Given that you are an admin 
> and click on the info-symbol of the dataset you should see the commandline.
>
> This is with a 18.05 Docker.
> Cheers,
> Bjoern
>
> Am 10.07.2018 um 08:58 schrieb Matthias Enders:
>> Dear Galaxy Community,
>>
>> is there any possibility to expose the command line call, generated 
>> within galaxy?
>>
>> We searched the net and found this discussions:
>> https://github.com/galaxyproject/galaxy/issues/3252
>> https://github.com/galaxyproject/galaxy/issues/2954
>>
>> But both are on the exposure to non-admin users. Within our instance 
>> we see the command line call nor for admin, neither for normal users!
>>
>> ...
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Re: [galaxy-dev] Expose Command Line in Galaxy

[Peter Cock]

There is a setting to enable showing the command line string
and full paths on disk via the "i" icon from a history entry, see

https://docs.galaxyproject.org/en/master/admin/options.html#expose-dataset-path

# This option allows users to see the full path of datasets via the
# "View Details" option in the history. This option also exposes the
# command line to non-administrative users. Administrators can always
# see dataset paths.
#expose_dataset_path: false

https://github.com/galaxyproject/galaxy/blob/release_18.05/config/galaxy.yml.sample#L1495

It existed in galaxy.ini too, which has since be replaced by
galaxy.yml

Peter

On Tue, Jul 10, 2018 at 8:19 AM, Matthias Enders
 wrote:
> Dear Björn,
>
> thanks for the very fast reply. Unfortunately, this part is not visible in 
> our instance. (see screenshot). As you can see in the topmost bar, this is 
> done, while being loged in as admin.
>
> Mit freundlichen Grüßen
>
> Matthias Enders
> ---
>
>
> GERMAN SEED ALLIANCE GmbH
> c/o Norddeutsche Pflanzenzucht
> Hans-Georg Lembke KG
> Hohenlieth, 24363 Holtsee
> Tel.: +49 (0)4351/ 736-189
> Fax: + 49 (0)4351/ 736-271
> Mobil: +49 (0)151/ 14247360
>
> Email: m.end...@german-seed-alliance.de
>
> Firmensitz Köln
> Amtsgericht Köln, HRB 73844
>
> -Ursprüngliche Nachricht-
> Von: Björn Grüning 
> Gesendet: Dienstag, 10. Juli 2018 09:15
> An: Matthias Enders ; 
> galaxy-dev@lists.galaxyproject.org
> Betreff: Re: [galaxy-dev] Expose Command Line in Galaxy
> Priorität: Hoch
>
> Hi Matthias,
>
> please have a look at the attached screenshot. Given that you are an admin 
> and click on the info-symbol of the dataset you should see the commandline.
>
> This is with a 18.05 Docker.
> Cheers,
> Bjoern
>
> Am 10.07.2018 um 08:58 schrieb Matthias Enders:
>> Dear Galaxy Community,
>>
>> is there any possibility to expose the command line call, generated
>> within galaxy?
>>
>> We searched the net and found this discussions:
>> https://github.com/galaxyproject/galaxy/issues/3252
>> https://github.com/galaxyproject/galaxy/issues/2954
>>
>> But both are on the exposure to non-admin users. Within our instance
>> we see the command line call nor for admin, neither for normal users!
>>
>> ...
___
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[galaxy-dev] Error with SAMTools Mpileup v1.2

[Aarthi Mohan]

Hi all,

I have a galaxy instance running 18.05 version. I recently installed 
'suite_samtools_1_2' (revision: 5b673ccc8747).  When I used 'Mpileup' tool, I 
ran into the below error, and the jobs fail.

Error message from UI:

This job was killed when Galaxy was restarted.  Please retry the job.

Error report from UI:

python: 
/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/galaxy_33.sh:
 line 61: 27021 Segmentation fault  (core dumped) python 
"/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/set_metadata_16ppzR.py"
 
"/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/registry.xml"
 
"/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/working/galaxy.json"
 
"/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_in_HistoryDatasetAssociation_74_dGoEXq,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_kwds_HistoryDatasetAssociation_74_ZgPen_,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_out_HistoryDatasetAssociation_74_OsySK1,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_results_HistoryDatasetAssociation_74_1NfJC0,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/files/000/dataset_74.dat,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_override_HistoryDatasetAssociation_74_vZTPWp"
 
"/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_in_HistoryDatasetAssociation_75_AoWnZx,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_kwds_HistoryDatasetAssociation_75_J8fJUV,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_out_HistoryDatasetAssociation_75_CXBh3u,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_results_HistoryDatasetAssociation_75_T_tzxr,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/files/000/dataset_75.dat,/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/metadata_override_HistoryDatasetAssociation_75_9fiQnm"
 5242880

>From galaxy.log file:

[LocalRunner.work_thread-1] execution finished: 
/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/database/jobs_directory/000/33/galaxy_33.sh
galaxy.model.metadata DEBUG 2018-07-10 17:31:51,417 [p:26910,w:1,m:0] 
[LocalRunner.work_thread-1] setting metadata externally failed for 
HistoryDatasetAssociation 74: External set_meta() not called
/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/.venv/bin/python: !!! uWSGI process 
26910 got Segmentation Fault !!!
*** backtrace of 26910 ***
/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/.venv/lib/python2.7/site-packages/uwsgi.so(uwsgi_backtrace+0x2e)
 [0x7fc5c385897e]
/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/.venv/lib/python2.7/site-packages/uwsgi.so(uwsgi_segfault+0x2f)
 [0x7fc5c3858d4f]
/lib64/libc.so.6(+0x35270) [0x7fc5ca0ba270]
/lib64/libc.so.6(strchrnul+0x1a) [0x7fc5ca11522a]
/lib64/libc.so.6(_IO_vfprintf+0x92) [0x7fc5ca0cc212]
/lib64/libc.so.6(+0x4c431) [0x7fc5ca0d1431]
/lib64/libc.so.6(_IO_vfprintf+0x1ee) [0x7fc5ca0cc36e]
/lib64/libc.so.6(+0xf6155) [0x7fc5ca17b155]
/lib64/libc.so.6(error+0xcd) [0x7fc5ca17b2ad]
/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/.venv/lib/python2.7/site-packages/pysam/./libcbcftools.so(main_vcfindex+0x504)
 [0x7fc5a9183bc4]
/home/aarthi/GALAXY/galaxy_18/galaxy_18.05/.venv/lib/python2.7/site-packages/pysam/libcutils.so(+0x14271)
 [0x7fc5a96da271]
/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6722) [0x7fc5cae514e2]
/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed) [0x7fc5cae53efd]
/lib64/libpython2.7.so.1.0(+0x70858) [0x7fc5caddd858]
/lib64/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fc5cadb89a3]
/lib64/libpython2.7.so.1.0(+0x5a995) [0x7fc5cadc7995]
/lib64/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fc5cadb89a3]
/lib64/libpython2.7.so.1.0(+0xa2ce7) [0x7fc5cae0fce7]
/lib64/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fc5cadb89a3]
/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x2336) [0x7fc5cae4d0f6]
/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed) [0x7fc5cae53efd]
/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x663c) [0x7fc5cae513fc]
/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed) [0x7fc5cae53efd]
/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x663c) [0x7fc5cae513fc]
/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x67bd) [0x7fc5cae5157d]
/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x67bd) [0x7fc5cae5157d]
/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed) [0x7fc5cae53efd]
/lib64/libpython2.7.so.1.0(+0x7094d) [0x7fc5caddd94d]
/lib64/libpython2.7.so.1.0(PyObject_Call+0x43) [0x7fc5cadb89a3]
/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x17fd) [0x7fc5cae4c5bd]
/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x67bd) [0x7fc5cae5157d]
/lib64/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x67bd) [0x7fc5cae5157d]
/lib64/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x7ed) [0x7fc5cae53efd]
/lib

Re: [galaxy-dev] Expose Command Line in Galaxy

[Hans-Rudolf Hotz]

Hi Matthias

If for whatever reasons the  "i" (view details) icon doesn't work for 
you, you can use the Galaxy Report Webapp (for docker installations see: 
https://github.com/bgruening/docker-galaxy-stable#Galaxy-Report-Webapp ) 
as an alternative.


You can find your (failed) job via "Jobs in error per day this month". 
Once you clicked on the 'job id' you will get the executed command line/



Hope this helps.
Regards, Hans-Rudolf





On 07/10/2018 08:58 AM, Matthias Enders wrote:

Dear Galaxy Community,

is there any possibility to expose the command line call, generated within 
galaxy?

We searched the net and found this discussions:
https://github.com/galaxyproject/galaxy/issues/3252
https://github.com/galaxyproject/galaxy/issues/2954

But both are on the exposure to non-admin users. Within our instance we see the 
command line call nor for admin, neither for normal users!

The problem, behind the question is the error message: "An invalid option was 
selected for database, 'myCoolDatabaseName', please verify." In Blast 
(toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastn_wrapper/0.2.01)

Local (directly from command line, without Galaxy in between) the blast works 
fine.

We are using the 18.05 Docker Galaxy Version.

Thanks in advance!

Mit freundlichen Grüßen

Matthias Enders
---


GERMAN SEED ALLIANCE GmbH
c/o Norddeutsche Pflanzenzucht
Hans-Georg Lembke KG
Hohenlieth, 24363 Holtsee
Tel.: +49 (0)4351/ 736-189
Fax: + 49 (0)4351/ 736-271
Mobil: +49 (0)151/ 14247360

Email: m.end...@german-seed-alliance.de

Firmensitz Köln
Amtsgericht Köln, HRB 73844

-Ursprüngliche Nachricht-
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galaxy-dev-requ...@lists.galaxyproject.org
Gesendet: Montag, 9. Juli 2018 18:00
An: galaxy-dev@lists.galaxyproject.org
Betreff: galaxy-dev Digest, Vol 145, Issue 3

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Today's Topics:

1. From Paste to uWSGI (Jochen Bick)
2. Re: From Paste to uWSGI (Peter Briggs)
3. Re: From Paste to uWSGI (Martin Čech)


--

Message: 1
Date: Mon, 9 Jul 2018 13:49:23 +0200
From: Jochen Bick 
To: "galaxy-dev@lists.galaxyproject.org"

Subject: [galaxy-dev] From Paste to uWSGI
Message-ID: <1a0f33ad-938c-64d5-8db8-28914a5ca...@usys.ethz.ch>
Content-Type: text/plain; charset="utf-8"; format=flowed

Hi all,

we would like to update to 18.05 and thereby also update our Paste Server.

https://docs.galaxyproject.org/en/latest/admin/scaling.html

Is there any tutorial on how to update from Paste to uWSGI?


Cheers 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



--

Message: 2
Date: Mon, 9 Jul 2018 15:31:16 +
From: Peter Briggs 
To: Jochen Bick ,
"galaxy-dev@lists.galaxyproject.org"

Subject: Re: [galaxy-dev] From Paste to uWSGI
Message-ID:

Content-Type: text/plain; charset="iso-8859-1"

Hello Jochen

I'm not aware of a tutorial but here are some observations from my (very) 
recent experiences upgrading a local paste-based 17.09 instance to a 
uwsgi-based 18.05 configuration. It's not comprehensive because the 
configuration will depend on decisions you need to make based on your local 
setup, but it might be helpful as a starting point.

Before beginning:

-- Commit to migrating from galaxy.ini to galaxy.yml (if not done previously)

Even though its possible to stick with the old galaxy.ini file, it seems best 
to move to the new format - my feeling is, probably the migration will have to 
happen at some point anyway, and also the documentation is more focussed on the 
newer galaxy.yml v