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_pyth... 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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