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 <dave@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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