[galaxy-dev] Looking for a running example of planemo test with options from_data_table

[Laure QUINTRIC]

Dear list,

Is there somewhere in the Galaxy any running example of a planemo test 
embracing a from_data_table option ?


We are trying to reproduce the picard example referenced here:
https://github.com/jmchilton/picard/commit/4df8974384081ee1bb0f97e1bb8d7f935ba09d73#diff-4145b3df5cbab370b2450e33dc343c3a

We also have a look on several examples on the IUC, unfortunately it 
seems to work only with values from history.


Many thanks,

Laure, Patrick and Olivier.
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Re: [galaxy-dev] Displaying tool select list according to user

[Laure QUINTRIC]

A workaround would be to do this :

- first, create a tool which will output a tabular loc file with all the 
custom banks for the connected user.
- then add in the ncbi_blast wrapper a select list with the attribute 
from_dataset to load the loc file generated by the previous tool  : see 
the example here : 
https://docs.galaxyproject.org/en/latest/dev/schema.html#from-dataset


I have something like this in the ncbi_blast tool:
    label="My custom dbs"/>
    optional="true" multiple="true" display="checkboxes" label="Select our 
custom db">

    
    
    
    
    

and I set in param userdb_loc_file the loc file which is in my history 
and looks like this :
NCBI_ntNCBI_nt 
2017-05-19/path/to/biobanks/n/NCBI_nt/current/NCBI_nt/NCBI_nt


Laure

Le 12/09/2017 à 17:25, Peter Cock a écrit :

Thanks Fred,

That's the previous discussion I was trying to find -
sadly no clear solution but some ideas to explore.

It does seem filtering example.loc by user or role
is not a niche request. I wonder if this could be
linked to the Galaxy data library permissions
structure as a way to manage the access rights?

Peter

On Tue, Sep 12, 2017 at 4:20 PM, SAPET, Frederic 
<frederic.sa...@biogemma.com <mailto:frederic.sa...@biogemma.com>> wrote:


Hi Laure,

There are others users (including me! ) that need this kind of
function :

http://dev.list.galaxyproject.org/Blast-db-permission-td4670440.html
<http://dev.list.galaxyproject.org/Blast-db-permission-td4670440.html>

@Galaxy team:

Do we need to add an issue in GitHub ?

Do you think that it could be enabled one day ?

I think this something that could be nice to develop !

I would be glad to help.

Thank a lot

Fred

*De :*galaxy-dev
[mailto:galaxy-dev-boun...@lists.galaxyproject.org
<mailto:galaxy-dev-boun...@lists.galaxyproject.org>] *De la part
de* Peter Cock
*Envoyé :* mardi 12 septembre 2017 14:56
*À :* Laure QUINTRIC <laure.quint...@ifremer.fr
<mailto:laure.quint...@ifremer.fr>>
*Cc :* Galaxy-dev <galaxy-dev@lists.galaxyproject.org
<mailto:galaxy-dev@lists.galaxyproject.org>>
*Objet :* Re: [galaxy-dev] Displaying tool select list according
to user

Hi Laure,

I don't think there is any easy to use mechanism for this in Galaxy.

Unfortunately Galaxy loads all the *.loc files at startup and treats

them as global values available to all users equally.

I can't find the email thread, but I recall someone previously trying

to do something with a single large example.loc file for all users

but with an extra column for filtering by account name. I forget if

they got these changes to work or not.

Assuming you only have a few separate versions of the example.loc

file, you could create copies of the BLAST wrapper XML file which

use the specific *.loc file - and then restrict the tool by user?

In either case at a minimum you would have to maintain local

changes to the BLAST wrappers (and potentially changes to

    Galaxy itself), which is not a good situation.

Peter

On Tue, Sep 12, 2017 at 1:41 PM, Laure QUINTRIC
<laure.quint...@ifremer.fr <mailto:laure.quint...@ifremer.fr>> wrote:

Hello Galaxy users,

I try to figure out how I can display a select list into a
galaxy tool according to the connected user.

I have several .loc files containing the paths for custom
blast databases I have created for several users (user1.loc,
user2.loc, and so on). I would like the blast tool to display
the specific databases for the connected user (user1 or user2).

Any idea on how to proceed ?
Regards,
Laure


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--
Laure QUINTRIC
IDM-RIC - Cellule Bio-informatique
02 98 22 49 11

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Re: [galaxy-dev] Displaying tool select list according to user

[Laure QUINTRIC]

Hi Peter,

Thank you for your answer. Maybe I should try your option below :

Le 12/09/2017 à 14:56, Peter Cock a écrit :


I can't find the email thread, but I recall someone previously trying
to do something with a single large example.loc file for all users
but with an extra column for filtering by account name. I forget if
they got these changes to work or not.


But in this case, did you remember how to write the filter to match the 
extra column with the username to the connected account name ? as he 
$__user_id__ variable could not be user between  tags ?


Laure

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[galaxy-dev] Displaying tool select list according to user

[Laure QUINTRIC]

Hello Galaxy users,

I try to figure out how I can display a select list into a galaxy tool 
according to the connected user.


I have several .loc files containing the paths for custom blast 
databases I have created for several users (user1.loc, user2.loc, and so 
on). I would like the blast tool to display the specific databases for 
the connected user (user1 or user2).


Any idea on how to proceed ?
Regards,
Laure


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Re: [galaxy-dev] Restart Galaxy without interruption

[Laure QUINTRIC]

Hi Gildas,

Have a look here : 
https://github.com/martenson/dagobah-training/tree/master/advanced/002a-systemd-supervisor


See ya.
Laure


Le 14/11/2016 à 21:35, Gildas Le Corguillé a écrit :

Hi,

Since Galaxy need to be restarted sometime (load datatype, add 
ressources in .loc, apply changes in the galaxy.ini), is anybody of 
you have solutions to restart it without interrupt the service?


We are now using nginx, uwsgi and supervisord.

My hope is to split the Galaxy process in two group (1 uwsgi and 2 job 
handlers per group). That way, we will be able to restart the group1 
and then the group2.



I was planning to set the 2 uwsgi servers and delegate the load 
balancing to ngnix 
(https://www.nginx.com/resources/admin-guide/load-balancer/)
But maybe, some of you already implemented that and can provide me 
some advices or warnings.


The job handler part seems easier to deal with
--server-name=handler1_%(process_num)s
--server-name=handler2_%(process_num)s

Thanks by advance

Gildas

-
Gildas Le Corguillé - Bioinformatician/Bioanalyste

Plateform ABiMS (Analyses and Bioinformatics for Marine Science)
http://abims.sb-roscoff.fr

Member of the Workflow4Metabolomics project
http://workflow4metabolomics.org 

Station Biologique de Roscoff - UPMC/CNRS - FR2424
Place Georges Teissier 29680 Roscoff FRANCE
tel: +33 2 98 29 23 81
--





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[galaxy-dev] dynamic runner and embed_metadata_in_job

[Laure QUINTRIC]

Hi Galaxy users,

As somebody try to run dynamic runner with the option 
embed_metadata_in_job set to False ?


I notice that it works with drmaa runner but not with dynamic.

Here is my job_conf.xmf :




python
my_conf
False



I also set the this parameter in galaxy.ini

retry_metadata_internally = True

But I still have the set_metadata.py script in my jobs.

Thanks for help.

Regards,

Laure

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[galaxy-dev] job_conf.xml and nativespecification

[Laure QUINTRIC]

Hi galaxy users,

while using galaxy with drmaa and real user on drm system, I would like 
to know if there's a way to set the variable PBS_O_LOGNAME to the real 
user name in the job_conf.xml :


-v PBS_O_LOGNAME=[REAL_USER_NAME??] -q 
test -l mem=100gb 


Thank you,

Laure

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[galaxy-dev] set_metadata in galaxy_XXX.sh script

[Laure QUINTRIC]

Hi there (sorry for all theses questions),

when I execute a job with remote user drmaa configuration on our pbs 
cluster, I see in the job working directory the script the galaxy_XXX.sh 
which set the galaxy virtual env and execute set_metadata.py after 
tool_script.sh completion but I get this in cluster error output :


python: /lib64/libz.so.1: no version information available (required by 
python)

Could not find platform dependent libraries 
Consider setting $PYTHONHOME to [:]
Traceback (most recent call last):
  File 
"galaxy/database/job_working_directory/002/2824/set_metadata_tkCRRk.py", 
line 1, in 
from galaxy_ext.metadata.set_metadata import set_metadata; 
set_metadata()
  File "galaxy/galaxy/lib/galaxy_ext/metadata/set_metadata.py", line 
15, in 

import json
ImportError: No module named json

The tool is execution is ok but the metadata script failed, but as that 
script is executed on the cluster and not on galaxy server, (I think) 
the virtual env is not properly set.


Is there a way to remove set_metadata from galaxy_XXX.sh script as It 
was in v16.01 ? I don't really understand what to set in galaxy.ini (I 
tried to set retry_metadata_internally to True and then False but I get 
the same result).


Regards,
Laure
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Re: [galaxy-dev] remote user CAS invalide session

[Laure QUINTRIC]

Thank you for your quick support.
Laure

Le 19/04/2016 19:05, Dannon Baker a écrit :
This turned out to be a problem with how the maildomain was handled 
after a recent fix to support API interactions bypassing remote user 
auth.


I'm working on a fix which you can follow and test here: 
https://github.com/galaxyproject/galaxy/pull/2195


Thanks again for the report!

On Tue, Apr 19, 2016 at 8:25 AM, Dannon Baker <dannon.ba...@gmail.com 
<mailto:dannon.ba...@gmail.com>> wrote:


Thank you for the report!  I'm able to reproduce this here on my
local test install and will try to figure out what's going on and
let you know when I have a fix.

-Dannon

On Tue, Apr 19, 2016 at 3:07 AM, Laure QUINTRIC
<laure.quint...@ifremer.fr <mailto:laure.quint...@ifremer.fr>> wrote:

Hi galaxy users,

I just installed version 16.04 of galaxy. I can connect to
galaxy with remote user through CAS authentification but my
session is invalidated, I get this message in the history :
An error occurred while getting updates from the server.
Please contact a Galaxy administrator if the problem persists.
Details

In paster.log, I can see this :

galaxy.web.framework.webapp WARNING 2016-04-18 17:37:47,308
User logged in as 't...@company.fr <mailto:t...@company.fr>'
externally, but has a cookie as 'toto' invalidating session

and just after I can see :

galaxy.web.framework.webapp WARNING 2016-04-18 17:37:48,018
User logged in as 'toto' externally, but has a cookie as
't...@company.fr <mailto:t...@company.fr>' invalidating session

It seems that variables remote_user_email and
galaxy_session.user.email ( in
galaxy/lib/web/framework/webapp.py) are set to
login@maildomain and then set to login only... so the user
login is not always the user email address.

In the config/galaxy.ini I set
remote_user_maildomain = company.fr <http://company.fr>
remote_user_header = HTTP_CAS_UID

Can you tell me how to go through this ? I did not have this
problem in v16.01.

Best regards




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[galaxy-dev] remote user CAS invalide session

[Laure QUINTRIC]

Hi galaxy users,

I just installed version 16.04 of galaxy. I can connect to galaxy with 
remote user through CAS authentification but my session is invalidated, 
I get this message in the history :
An error occurred while getting updates from the server. Please contact 
a Galaxy administrator if the problem persists. Details 


In paster.log, I can see this :

galaxy.web.framework.webapp WARNING 2016-04-18 17:37:47,308 User logged 
in as 't...@company.fr' externally, but has a cookie as 'toto' 
invalidating session


and just after I can see :

galaxy.web.framework.webapp WARNING 2016-04-18 17:37:48,018 User logged 
in as 'toto' externally, but has a cookie as 't...@company.fr' 
invalidating session


It seems that variables remote_user_email and galaxy_session.user.email 
( in galaxy/lib/web/framework/webapp.py) are set to login@maildomain and 
then set to login only... so the user login is not always the user email 
address.


In the config/galaxy.ini I set
remote_user_maildomain = company.fr
remote_user_header = HTTP_CAS_UID

Can you tell me how to go through this ? I did not have this problem in 
v16.01.


Best regards



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