Re: [galaxy-dev] Building tool dependencies

[Matthias De Smet]

Hi All!

Thanks for chiming in! I’ll give the conda recipe approach a go, this seems to 
be the easiest way to go, and the most futureproof!

Thanks!

M

> Message: 1
> Date: Tue, 5 Jul 2016 06:56:00 +
> From: Matthias De Smet <matthias.des...@ugent.be>
> To: "galaxy-dev@lists.galaxyproject.org"
>   <galaxy-dev@lists.galaxyproject.org>
> Subject: Re: [galaxy-dev] Building tool dependencies
> Message-ID: <d70eed58-f05e-4084-9323-1b78c707b...@ugent.be>
> Content-Type: text/plain; charset="utf-8"
> 
> 
>> 
>> 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
>> 
> 
> 
> ----------
> 
> Message: 2
> Date: Tue, 5 Jul 2016 09:33:09 +0200
> From: Peter van Heusden <p...@sanbi.ac.za>
> To: galaxy-...@lists.bx.psu.edu
> Subject: Re: [galaxy-dev] Building tool dependencies
> Message-ID:
>   <cak1rexih9jxq19gysxdkdr6ync9azgabkfzxaktfm0m+tc2...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
> 
> 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 <matthias.des...@ugent.be> 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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> Message: 3
> Date: Tue, 5 Jul 2016 08:49:54 +0100
> From: Peter Briggs <peter.bri...@manchester.ac.uk>
> To: galaxy-dev@lists.galaxyproject.org
> Subject: Re: [galaxy-dev] Building tool dependencies
> Message-ID: <577b66a2.60...@manchester.ac.uk>
> Content-Type: text/plain; charset=utf-8; format=flowed
> 
> 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="e01853dfe111f3aea005315573400b72

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
> >
>
> ___
> Please keep all replies on the list by using "reply all"
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> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
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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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