That indeed looks like a better solution. I'll use the workaround for now
and update once setup_python_environment is implemented.


On 25 June 2014 13:33, Björn Grüning <bjoern.gruen...@gmail.com> wrote:

> Hi Janis,
>
> that is not working and it is currently not clear if we will change it.
> Please see the following Trello Card:
>
> https://trello.com/c/NsLJv9la/61-clean-up-tool-shed-setup-actions
>
> One of my project during the upcoming GCC hackathon is to implement a
> setup_python_environment, like the R, perl or ruby ones. With that in place
> your use case will be easy to implement. If you get your python package up
> and running at that time, this would be great!
>
> Cheers,
> Bjoern
>
> Am 24.06.2014 18:57, schrieb Jan Kanis:
>
>> Ok, here is the tool_dependencies.xml. This
>> <https://gist.github.com/JanKanis/650c88001c03ac4320fe#
>> file-not_working_tool_dependencies>
>>
>> (also attached, if that survives the list) is what I would like my
>> tool_dependencies.xml to look like, but it doesn't work because the
>> installation of lxml fails, as it can't find the libxml2 headers. I am now
>> using this
>> <https://gist.github.com/JanKanis/42b9cace27b9693a0677#
>> file-workaround_tool_dependencies-xml>
>>
>> as a workaround. It works because lxml is installed from a shell_command
>> which does include the variables set from the set_environment_for_install
>> block. This is from the blast2html tool.
>>
>> Jan
>>
>>
>> On 24 June 2014 15:30, Dave Bouvier <d...@bx.psu.edu> wrote:
>>
>>  Jan,
>>>
>>> In order to help track down this issue, could you provide the
>>> tool_dependencies.xml you're using?
>>>
>>>    --Dave B.
>>>
>>>
>>> On Tue 24 Jun 2014 05:40:30 AM EDT, Jan Kanis wrote:
>>>
>>>  In a tool_dependency.xml file I want to install python package lxml in
>>>> a virtual environment, as a tool I'm building needs it. The python
>>>> lxml package requires the libxml2 tool dependency. I have added a
>>>> set_environment_for_install action that refers to the libxml2
>>>> repository, but when python/pip tries to install lxml it fails,
>>>> apparently because it can't find the required headers. This appears to
>>>> be because the setup_virtualenv action does not include install
>>>> environment variables.
>>>>
>>>> It seems to me that install environment variables should be sourced
>>>> for every following action that can do nontrivial things, not just
>>>> shell commands.
>>>>
>>>> Alternatively, am I trying to install lxml the wrong way, is there a
>>>> better way? (I'm running on python 2.6)
>>>>
>>>> Jan
>>>>
>>>>
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>>
>>
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