Re: [galaxy-dev] Conda: confused dependencies with multiple R versions and rpy

[Marius van den Beek]

Hi Steve,

The scatterplot tool is relatively old and has not had its dependencies
updated to be conda compatible.
https://github.com/galaxyproject/tools-devteam/blob/master/tools/scatterplot/scatterplot.xml

The relevant lines are these:

  
numpy
rpy
   wrote:

> Hi,
>   trying to get my tools going, part 29.  I have a Docker image with the
> latest Galaxy release, patched to fix the Conda install bug I found
> earlier, my tools are installed ok and I’ve added a few from the toolshed
> for good measure.
>
> One of my tools requires R 3.0.2 which is installed ok.   I also installed
> scatterplot from the toolshed which requires R 2.11; that is also installed
> ok by conda. However, I get this message when trying to run scatterplot:
>
> Traceback (most recent call last):
>   File 
> "/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/d243056b22ed/scatterplot/scatterplot.py",
>  line 5, in 
> from rpy import *
>   File 
> "/tool_deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py",
>  line 134, in 
> """ % RVERSION)
> RuntimeError: No module named _rpy3002
>
>   RPy module can not be imported. Please check if your rpy
>   installation supports R 3.0.2. If you have multiple R versions
>   installed, you may need to set RHOME before importing rpy. For
>   example:
>
>   >>> from rpy_options import set_options
>   >>> set_options(RHOME='c:/progra~1/r/rw2011/')
>   >>> from rpy import *
>
>
> So it seems that rpy is installed and is aware of one version of R but not
> the other, and the other is being found (perhaps because it’s the default
> install in the Docker image?)
>
> FYI my docker image recipe is here:
>
> https://github.com/Alveo/docker-galaxy-alveo
>
> and the image itself is here:
>
> https://hub.docker.com/r/stevecassidy/alveo-galaxy/
>
> Any pointers to the way forward appreciated.
>
> Thanks,
> Steve
> —
> Department of Computing, Macquarie University
> http://web.science.mq.edu.au/~cassidy
>
>
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Re: [galaxy-dev] Conda: confused dependencies with multiple R versions and rpy

[Marius van den Beek]

Forgot to paste the link:
https://github.com/galaxyproject/tools-devteam/issues/385

On 1 September 2016 at 11:08, Marius van den Beek 
wrote:

> Hi Steve,
>
> The scatterplot tool is relatively old and has not had its dependencies
> updated to be conda compatible.
> https://github.com/galaxyproject/tools-devteam/
> blob/master/tools/scatterplot/scatterplot.xml
>
> The relevant lines are these:
>
>   
> numpy
> rpy
>   
>
>
> So it would attempt to get the R version via the rpy package. So my guess
> is that there is no rpy(1)
> package in conda. We can try to update the tool to use rpy2 and hope that
> that'll just work,
> and if that doesn't work we can explicitly add a requirement on R (which
> we can get through conda).
> I've opened an issue here:
>
> Best,
> Marius
>
> On 1 September 2016 at 09:50, Steve Cassidy 
> wrote:
>
>> Hi,
>>   trying to get my tools going, part 29.  I have a Docker image with the
>> latest Galaxy release, patched to fix the Conda install bug I found
>> earlier, my tools are installed ok and I’ve added a few from the toolshed
>> for good measure.
>>
>> One of my tools requires R 3.0.2 which is installed ok.   I also
>> installed scatterplot from the toolshed which requires R 2.11; that is also
>> installed ok by conda. However, I get this message when trying to run
>> scatterplot:
>>
>> Traceback (most recent call last):
>>   File 
>> "/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/d243056b22ed/scatterplot/scatterplot.py",
>>  line 5, in 
>> from rpy import *
>>   File 
>> "/tool_deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py",
>>  line 134, in 
>> """ % RVERSION)
>> RuntimeError: No module named _rpy3002
>>
>>   RPy module can not be imported. Please check if your rpy
>>   installation supports R 3.0.2. If you have multiple R versions
>>   installed, you may need to set RHOME before importing rpy. For
>>   example:
>>
>>   >>> from rpy_options import set_options
>>   >>> set_options(RHOME='c:/progra~1/r/rw2011/')
>>   >>> from rpy import *
>>
>>
>> So it seems that rpy is installed and is aware of one version of R but
>> not the other, and the other is being found (perhaps because it’s the
>> default install in the Docker image?)
>>
>> FYI my docker image recipe is here:
>>
>> https://github.com/Alveo/docker-galaxy-alveo
>>
>> and the image itself is here:
>>
>> https://hub.docker.com/r/stevecassidy/alveo-galaxy/
>>
>> Any pointers to the way forward appreciated.
>>
>> Thanks,
>> Steve
>> —
>> Department of Computing, Macquarie University
>> http://web.science.mq.edu.au/~cassidy
>>
>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>
>
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[galaxy-dev] Conda: confused dependencies with multiple R versions and rpy

[Steve Cassidy]

Hi,
  trying to get my tools going, part 29.  I have a Docker image with the latest 
Galaxy release, patched to fix the Conda install bug I found earlier, my tools 
are installed ok and I’ve added a few from the toolshed for good measure.

One of my tools requires R 3.0.2 which is installed ok.   I also installed 
scatterplot from the toolshed which requires R 2.11; that is also installed ok 
by conda. However, I get this message when trying to run scatterplot:


Traceback (most recent call last):
  File 
"/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/scatterplot/d243056b22ed/scatterplot/scatterplot.py",
 line 5, in 
from rpy import *
  File 
"/tool_deps/rpy/1.0.3/devteam/package_rpy_1_0_3/82170c94ca7c/lib/python/rpy.py",
 line 134, in 
""" % RVERSION)
RuntimeError: No module named _rpy3002

  RPy module can not be imported. Please check if your rpy
  installation supports R 3.0.2. If you have multiple R versions
  installed, you may need to set RHOME before importing rpy. For
  example:

  >>> from rpy_options import set_options
  >>> set_options(RHOME='c:/progra~1/r/rw2011/')
  >>> from rpy import *


So it seems that rpy is installed and is aware of one version of R but not the 
other, and the other is being found (perhaps because it’s the default install 
in the Docker image?)

FYI my docker image recipe is here:

https://github.com/Alveo/docker-galaxy-alveo

and the image itself is here:

https://hub.docker.com/r/stevecassidy/alveo-galaxy/

Any pointers to the way forward appreciated.

Thanks,
Steve
—
Department of Computing, Macquarie University
http://web.science.mq.edu.au/~cassidy

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