Re: [galaxy-dev] datatype dependencies

[Igor Topcin]

Hi guys,

Noticed that this thread had no further replies. I was wondering if this is
going to be in the road map for galaxy next releases. Would be very helpful
for sniffing and parsing complex datasets such as medical images.

Cheers,
Igor
On Jul 18, 2014 12:42 PM, Peter Cock p.j.a.c...@googlemail.com wrote:

 On Fri, Jul 18, 2014 at 4:21 PM, Eric Rasche rasche.e...@yandex.ru
 wrote:
  On 07/18/2014 09:49 AM, John Chilton wrote:
  My understanding of the code is that tool shed dependencies (or local
  dependencies) will not be available to tool shed datatypes (for
  sniffing for instance). Sorry.
 
  I figured as much, not very surprising at all. Dependencies
  notwithstanding, the idea has some modicum of merit. There are plenty of
  people who have already written great parsers that throw up errors, why
  should datatypes re-write them?

 Exactly - Trello request for the toolshed to handle both Python and
 binary dependencies for datatypes?

 (e.g. samtools is a binary dependency of the SAM/BAM datatypes,
 used for conversion and indexing)

  If you want to hack up your local instance to resolve dependencies
  during the sniffing process that may be possible - my guess is you
  could add requirement tags to tools/data_source/upload.xml and the
  __SET_METADATA__ tool definition embedded in
  lib/galaxy/datatypes/registry.py - though I have not tried this.
 
  Well heck, at that point I'd just use the fact that I know I'm in
  lib/galaxy/datatypes to locate the BioPython dependency that was
  installed through greps, globs, and finds. Though I'll hold off on that
  for a better solution.

 I'd manually install the Python dependencies as part of the Python
 used to run Galaxy itself?

 Peter
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[galaxy-dev] Trimmomatic wrapper for Galaxy

[Peter Cock]

Hi Simon,

I was looking for a Trimmomatic wrapper for Galaxy (which I have thus
far only used at the command line outside of Galaxy), and while there
does not seem to be one in the main Tool Shed, I see you have been
working on this over on the Test Tool Shed:

https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/trimmomatic_0_22
https://testtoolshed.g2.bx.psu.edu/view/simon-gladman/trimmomatic_032

Note that according to http://www.usadellab.org/cms/?page=trimmomatic
the Trimmomatic authors have been given permission to redistribute
the Illumina adapter sequences now :)

It would be nice to have functional tests, but other than that, what
status is the wrapper? Are there some issues blocking releasing this
via the main Tool Shed for wider use?

Thanks,

Peter
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[galaxy-dev] Help testing Galaxy - new release is coming soon

[Björn Grüning]

Hi!

As far as I know the Galaxy team is preparing a new release for next
week with a ton of great new features, like Interactive Environments,
multiple History view, Dataset collections and many more ...

If you want to help testing, trying out the latest features or just give
feedback we have put together a Galaxy Docker Image with all this stuff
included.

Install Docker, run the following command and report any issues!

docker run -p 8080:80 -p 8800:8800 --privileged bgruening/galaxy-stable:dev

Happy testing and Thanksgiving to everyone!
The Galaxy Docker Team
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