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

[nsora...@tiscali.it]

Dear Laure,have a look at 
https://github.com/galaxyproject/tools-devteam/blob/master/tools/bowtie_wrappers/bowtie_wrapper.xml
Cheers,Nicola
-- Messaggio originale--Da: Laure QUINTRICData: gio 15 feb 2018 16:06A: 
galaxy-dev@lists.galaxyproject.org;CC: Patrick Durand;Olivier 
Inizan;Oggetto:[galaxy-dev] Looking for a running example of planemo test with 
options from_data_table
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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[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] bigwig problem

[Nate Coraor]

Hi Jochen,

I ran in to this yesterday, we're working on fixing it right now. It's due
to this:

https://github.com/bioconda/bioconda-recipes/issues/5430

And because Galaxy's converters use the `ucsc_tools` IUC conda metapackage,
which still points to the old versions. I have an update here:

https://github.com/galaxyproject/conda-iuc/pull/14

Once that is available you should be able to `conda update ucsc_tools` the
affected environments. I am also working on switching all of the
requirements so they depend on the individual ucsc-* packages from Bioconda
instead of the metapackage so we shouldn't need to maintain it in the
future.

--nate

On Thu, Feb 15, 2018 at 10:17 AM, Jochen Bick 
wrote:

> Hi,
>
> how can I fix this problem?
>
> bedGraphToBigWig: error while loading shared libraries:
> libmysqlclient.so.18: cannot open shared object file: No such file or
> directory
>
> I have the files in the local bin but somehow it does not work inside
> galaxy.
>
> Thanks in advance.
> Cheers
> Jochen
>
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[galaxy-dev] bigwig problem

[Jochen Bick]

Hi,

how can I fix this problem?

bedGraphToBigWig: error while loading shared libraries: libmysqlclient.so.18: 
cannot open shared object file: No such file or directory

I have the files in the local bin but somehow it does not work inside galaxy.

Thanks in advance.
Cheers
Jochen

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Re: [galaxy-dev] Running toolshed on localhost is broken in release_17.09?

[Peter Briggs]

Hello Nate

Thanks for looking into this so quickly - I've manually applied the patch in 
your PR for toolshed.yml.sample and that works perfectly, thanks!

Re picking up older .ini config files for a toolshed instance: what I was doing 
was spinning up a completely new pair of Galaxy and toolshed instances on my 
local machine, just for testing purposes. So in this case there was no 
pre-existing .ini files to be picked up.

Hope that makes sense - thanks again for your help, and the patch.

Best wishes

Peter

--
Peter Briggs peter.bri...@manchester.ac.uk
Bioinformatics Core Facility University of Manchester
B.1083 Michael Smith Bldg Tel: (0161) 2751482


From: Nate Coraor [n...@bx.psu.edu]
Sent: Wednesday, February 14, 2018 4:19 PM
To: Peter Briggs
Cc: galaxy-dev@lists.galaxyproject.org
Subject: Re: [galaxy-dev] Running toolshed on localhost is broken in 
release_17.09?

Hi Peter,

This might be due to the switch from Paste to uWSGI for reports and tool shed 
applications in 17.09. I do see that when using the 17.09 default configuration 
(uWSGI with config/tool_shed.yml.sample), the static content is not configured 
to be served, so I submitted a fix for that here:

https://github.com/galaxyproject/galaxy/pull/5534

However, if you have an existing tool_shed.ini, run_tool_shed.sh is supposed to 
continue to use Paste, and since run_tool_shed.sh (presumably) decided to start 
with uWSGI instead of Paste, it did not find your tool_shed.ini. Is it located 
somewhere other than config/tool_shed.ini?

--nate

On Wed, Feb 14, 2018 at 9:34 AM, Peter Briggs 
> wrote:
Hello

I'm trying to run a toolshed instance on localhost to test some local tool 
changes - this works okay in release_17.05, but setting one up using 
release_17.09 appears to be broken out of the box, at least for me.

In release_17.09, after configuration connecting to http://127.0.0.1:9009/ 
brings up a version which isn't usable - the styles are missing and it it's not 
possible to navigate, register/login etc.

Uncommenting lines like

  # Serving static files (needed if running standalone)
  static_enabled: True

in the config/tool_shed.yml file don't seem to make any difference.

I didn't find anything in the Galaxy Github issue list about this, so has 
anyone else observed this behaviour? For now I've just gone back to 
release_17.05 for my local toolshed needs.

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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