Re: [galaxy-dev] Dependencies issue with tool installation via ephemeris

2017-09-13 Thread Björn Grüning


On 14.09.2017 00:10, RMSe17 wrote:
> Bjoern,
> 
> Looks like some tools install fine without the
> "install_tool_dependencies: True" but others come up with dependencies
> missing.  I wonder if some tools are older and are missing something
> in conda?  That's just a guess on my part.

This can very well be! Which tool is this?

Cheers,
Bjoern

> Using 17.01 latest, so yea defaults could be different.

17.05 is recent and 17.09 will be released soon!

Cheers,
Bjoern

> Thanks!
> 
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Re: [galaxy-dev] Galaxy server requires a restart to activate tools

2017-09-13 Thread Björn Grüning
Hi,

afaik Marius fixed a few bugs in 17.05 and I know that 17.05 should work
as described not sure 17.01 can be exprected to work this way.

Can you try 17.05?
Thanks,
Bjoern

On 14.09.2017 03:51, RMSe17 wrote:
> Hello, I have a fresh 17.01 Galaxy installed and set up with uWSGI.
> After installing a new tool, I can't run it without first restarting
> Galaxy.  This is odd, because I know in 17.01 that should no longer be
> happening.
> 
> The error I get is "This tool was disabled before job completed.
> Please contact your Galaxy administrator.
> 
> In the logs I see "Tool (... tool name) removed from tool config,
> unable to run job
> Cleaning up external metadata files
> Error checking job readiness"
> 
> After Galaxy restarts, the tool runs fine.
> 
> Is there anything typical that could cause this?  Any place I should
> start looking?
> 
> Thanks!
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[galaxy-dev] Galaxy server requires a restart to activate tools

2017-09-13 Thread RMSe17
Hello, I have a fresh 17.01 Galaxy installed and set up with uWSGI.
After installing a new tool, I can't run it without first restarting
Galaxy.  This is odd, because I know in 17.01 that should no longer be
happening.

The error I get is "This tool was disabled before job completed.
Please contact your Galaxy administrator.

In the logs I see "Tool (... tool name) removed from tool config,
unable to run job
Cleaning up external metadata files
Error checking job readiness"

After Galaxy restarts, the tool runs fine.

Is there anything typical that could cause this?  Any place I should
start looking?

Thanks!
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Re: [galaxy-dev] Dependencies issue with tool installation via ephemeris

2017-09-13 Thread RMSe17
Bjoern,

Looks like some tools install fine without the
"install_tool_dependencies: True" but others come up with dependencies
missing.  I wonder if some tools are older and are missing something
in conda?  That's just a guess on my part.

Using 17.01 latest, so yea defaults could be different.

Thanks!
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Re: [galaxy-dev] Dependencies issue with tool installation via ephemeris

2017-09-13 Thread Björn Grüning
Hi,

On 13.09.2017 21:15, RMSe17 wrote:
> Thanks for your help Bjorn, I was already setting
> install_resolver_dependencies to True, but I looked at the example you
> referenced, and saw couple other options that I didn't have set (I
> didn't see them mentioned in the ephemeris documentation).
> 
> Once I set the following in the tools yml list, everything started
> working correctly.
> install_tool_dependencies: True

This should not be needed, it will install old tool dependencies, which
are deprecated.

Which Galaxy version are you using, depending on this the defaults might
change.

Cheers,
Bjoern

> install_repositoty_dependencies: True
> 
> Interestingly according to the comments in the example, these should
> be defaulting to true anyway, but I had to set them explicitly.
> 
> Thanks again for your help!
> 
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Re: [galaxy-dev] Dependencies issue with tool installation via ephemeris

2017-09-13 Thread RMSe17
Thanks for your help Bjorn, I was already setting
install_resolver_dependencies to True, but I looked at the example you
referenced, and saw couple other options that I didn't have set (I
didn't see them mentioned in the ephemeris documentation).

Once I set the following in the tools yml list, everything started
working correctly.
install_tool_dependencies: True
install_repositoty_dependencies: True

Interestingly according to the comments in the example, these should
be defaulting to true anyway, but I had to set them explicitly.

Thanks again for your help!
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[galaxy-dev] Cron Job Tool

2017-09-13 Thread Mohamed Kassam
Dear all,

I made a tool that is doing analysis every two days and send me a
notification by email when the analyis is completed.

I would like to know if I can run this kind of job and how  to integrate
this tool in Galaxy tools panel  in Galaxy ? If someone has this experience
can help me.


Thanks in advance,

Mohamed
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[galaxy-dev] tool runtimes

2017-09-13 Thread Matthias Bernt

Dear list,

I have the impression that on our cluster the "auxiliary" computations 
(e.g. setting metadata) is very slow (minutes) compared to the run time 
of the actual tools (often just seconds).


Do you have any suggestion how I can tweak this or how I can analyze 
this more detailed?


Best,
Matthias

--

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

2017-09-13 Thread 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 
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


@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
] *De la part
de* Peter Cock
*Envoyé :* mardi 12 septembre 2017 14:56
*À :* Laure QUINTRIC mailto:laure.quint...@ifremer.fr>>
*Cc :* Galaxy-dev 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
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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