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 $INSTALL_DIR/bin
which should avoid installing to /usr/bin.
You'll then need to do something like:
<action type="set_environment">
<environment_variable action="prepend_to"
name="PYTHONPATH">$INSTALL_DIR/lib/python</environment_variable>
<environment_variable action="prepend_to"
name="PATH">$INSTALL_DIR/bin</environment_variable>
...
</action>
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:
...
<action type="setup_python_environment">
<repository name="package_python_2_7_10" owner="iuc">
<package name="python" version="2.7.10" />
</repository>
<package
sha256sum="e01853dfe111f3aea005315573400b7216ddbabbf1f28d482a71217d67ae4f81">https://pypi.python.org/packages/source/p/pandas/pandas-0.16.2.tar.gz</package>
...
(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 <action
type="download_by_url”> and <action type=“create_virtualenv”> actions, but I’m not
really sure that’s the way to go. I havent found any real resources on how to build package
dependencies either.
Any help? Now, approaching it by downloading the package from github with <action
type="download_by_url”> and installing it with <action type="shell_command">python
setup.py install</action>. 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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