[galaxy-dev] July Galactic News: GCC2016, GCC2017(!), Admin/Dev Trainings, GAMe 2017!

[Dave Clements]

Hello all,

Some highlights from the *July Galaxy News
:*

   -

   GCC2016 is done!
   
and
   slides and posters are now online (and video and training materials are
   coming)
   - And there is plenty more happening:
  -

  *GCC2017 Announced
  
!*
  -

  Swiss-German Galaxy Days
  

  -

  Galaxy Admin Training
  

   announced
  -

  European Galaxy Developer Knowledge Exchange
  

  -

  Galaxy AustralAsia Meeting (GAMe 2017)
  

   announced
  -

  Other Upcoming Events
  
  -

   82 new Papers
   
   -

   Open positions
   
   -

   New public
   

and semi-public
   

Galaxy
   servers
   -

   A new community log board entry
   
   -

   New Releases
   :
   blend4php
   
   , Planemo
   ,
   and galaxy-lib
   

   -

   And other news
    too.

Hope to see you in Montpellier

!

Dave Clements and the Galaxy Team



-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/
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Re: [galaxy-dev] Using operations on multiple datasets

[Björn Grüning]

Hi,

Am 05.07.2016 um 23:18 schrieb D K:
> Sorry for the crosspost to Biostars, but I didn't get a response, so I
> thought I'd post here:
> 
> I just noticed that Galaxy allows creation of lists of datasets by clicking
> on the "Operations on multiple datasets" in the history panel. How does one
> use this with a custom tool (e.g. what does one put between the 
>  tags). Is the list treated as a text file with a list of each
> file? I couldn't find any examples or documentation online. I'd appreciate
> it if someone could point me in the right direction.

You can not use this feature in a tool, it's pure UI. But you can use
multiple="True"

https://github.com/galaxyproject/tools-iuc/blob/180a403421967d36f995941b1a4561349d75cfc5/tools/mothur/merge.files.xml#L32

maybe this helps?
Cheers,
Bjoern

> Thanks!
> 
> 
> 
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Re: [galaxy-dev] Building tool dependencies

[Peter Briggs]

Hello Matthias

From what I've seen there are a number of different recipes used for 
installing Python packages via the toolshed; the approach you're using 
seems to be pretty common. In these cases the usual 'shell_command' 
seems to be:


python setup.py install --install-lib $INSTALL_DIR/lib/python 
--install-scripts $INSTALL_DIR/bin


which should avoid installing to /usr/bin.

You'll then need to do something like:


  name="PYTHONPATH">$INSTALL_DIR/lib/python
  name="PATH">$INSTALL_DIR/bin

  ...


to ensure that the correct environment is set up when the tool is used.

Aside from this: elsewhere I've seen other approaches including a 
"magic" "package" command where the whole download and install is taken 
care of in a single tag. For example:


...

  
 
   
   sha256sum="e01853dfe111f3aea005315573400b7216ddbabbf1f28d482a71217d67ae4f81">https://pypi.python.org/packages/source/p/pandas/pandas-0.16.2.tar.gz

...

(see 
https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_python_2_7_pandas_0_16/tool_dependencies.xml 
for the full recipe that I've pulled this fragment from.)


HTH

Best wishes

Peter

On 05/07/16 07:56, Matthias De Smet wrote:




Hi

I’m trying to put together a tool + dependency package to use umi-tools 
(https://github.com/CGATOxford/UMI-tools) from Galaxy.
I’m at a loss on how I should organise this.

The package is available from either github or pip. Which one is preferable to use? How do I  
make sure the package dependencies are installed? I’ve found the  and installing it with python 
setup.py install. This, however, tries to install the package to /usr/bin/ which isn’t desirable 
(obviously).

Thanks a lot!
M



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--
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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Re: [galaxy-dev] Building tool dependencies

[Peter van Heusden]

Actually, for recent Galaxy, I'd recommend making a conda recipe for
UMI-tools and contributing it to bioconda:

https://bioconda.github.io/

Then your tool can just depend on this and the conda dependency resolver
(default in Galaxy since 16.01) can find it. Others can comment on the
recent work on conda/toolshed integration.

Peter

On 5 July 2016 at 08:56, Matthias De Smet  wrote:

>
> >
> > Hi
> >
> > I’m trying to put together a tool + dependency package to use umi-tools (
> https://github.com/CGATOxford/UMI-tools) from Galaxy.
> > I’m at a loss on how I should organise this.
> >
> > The package is available from either github or pip. Which one is
> preferable to use? How do I  make sure the package dependencies are
> installed? I’ve found the  and installing it with  type="shell_command">python setup.py install. This, however, tries
> to install the package to /usr/bin/ which isn’t desirable (obviously).
> >
> > Thanks a lot!
> > M
> >
>
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Re: [galaxy-dev] Building tool dependencies

[Matthias De Smet]

> 
> Hi
> 
> I’m trying to put together a tool + dependency package to use umi-tools 
> (https://github.com/CGATOxford/UMI-tools) from Galaxy.
> I’m at a loss on how I should organise this.
> 
> The package is available from either github or pip. Which one is preferable 
> to use? How do I  make sure the package dependencies are installed? I’ve 
> found the  and installing it with  type="shell_command">python setup.py install. This, however, tries 
> to install the package to /usr/bin/ which isn’t desirable (obviously).
> 
> Thanks a lot!
> M
> 

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