On Mon, Sep 23, 2013 at 12:51 PM, Björn Grüning
> Hi Carlos!
>> I have created a tool that depends on biopython. I don't like the idea
>> of having several copies of biopython around and also for best
>> practice making workflows using my tool reproducible, I chose to make
>> my package repository dependent of package_biopython_1_62.
> Cool thanks! I think that is best practise!
I disagree strongly. This is not a good idea. My thought is if you are
using a virtualenv, you shouldn't be trying to compose it with other
python dependencies - to me the whole point of virtualenv is that it
creates isolated little environments. I am not sure why duplicating
the biopython install reduces reproduciblity.
If you want to use individual Python packages using Galaxy's
dependency mechanism, I think you should then package them up one at a
time and hand modify PYTHONPATH and PATH - the way biopython is done.
Galaxy should have a separate action to make this easy, say
install_pip or something like that, as outlined by James Taylor at
>> I'm installing my package using the virtualenv option. As you can see
>> below I marked biopython as prior_installation_required="True".
>> However, I can see that virtualenv is installing a copy of biopython
>> in 'venv' under my tool install(see below). This doesn't sound right.
>> I was expecting that by making my repository dependent of biopython's
>> one that source would be used in my tool.
> Can you try to insert that (maybe adopt, its not checked):
> <action type="set_environment_for_install">
> <repository name="package_biopython_1_62" owner="biopython">
> <package name="biopython" version="1.62" />
> Only with that the PYTHONPATH is populated.
>> My plan is to create any non-existing "Tool dependency definition"
>> repository for every package my tool requires. This way you can always
>> count the same version of any of these packages is being used. I
>> thought that was the point, right?
>> Full ool_dependencies.xml:
>> <?xml version="1.0"?>
>> <package name="biopython" version="1.62">
>> <repository changeset_revision="ac9cc2992b69"
>> name="package_biopython_1_62" owner="biopython"
>> toolshed="http://testtoolshed.g2.bx.psu.edu" />
>> <package name="ngs-tools" version="0.1.6">
>> <install version="1.0">
>> <action type="setup_virtualenv">ngs-tools==0.1.6</action>
>> Contents of site-packages in my tool install dir:
>> $ ls -1
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> Please keep all replies on the list by using "reply all"
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> and other Galaxy lists, please use the interface at:
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