Am Montag, den 23.09.2013, 12:57 -0500 schrieb John Chilton: > On Mon, Sep 23, 2013 at 12:51 PM, Björn Grüning > <bjoern.gruen...@pharmazie.uni-freiburg.de> wrote: > > Hi Carlos! > > > >> Hi, > >> > >> 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[1] dependent of package_biopython_1_62. > >> > >> [1]http://testtoolshed.g2.bx.psu.edu/view/cjav/package_ngs_tools_0_1_6 > > > > 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 > some point.
Hi John, interesting point. What is the specific difference between venv and the pip installation? In which case do you propose to use which method? I never thought about different 'isolation-levels' (venv vs. the rest of the toolshed). We need to document somehow the use cases if we have different methods for python installations. Ciao, Bjoern > -John > > > > >> 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" /> > > </repository> > > </action> > > > > 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? > > > > Yes! > > > >> Full ool_dependencies.xml: > >> <?xml version="1.0"?> > >> <tool_dependency> > >> <package name="biopython" version="1.62"> > >> <repository changeset_revision="ac9cc2992b69" > >> name="package_biopython_1_62" owner="biopython" > >> prior_installation_required="True" > >> toolshed="http://testtoolshed.g2.bx.psu.edu"; /> > >> </package> > >> <package name="ngs-tools" version="0.1.6"> > >> <install version="1.0"> > >> <actions> > >> <action type="setup_virtualenv">ngs-tools==0.1.6</action> > >> </actions> > >> </install> > >> </package> > >> </tool_dependency> > >> > >> Contents of site-packages in my tool install dir: > >> $ ls -1 > >> shed_tools_dependencies.central/ngs-tools/0.1.6/cjav/package_ngs_tools_0_1_6/3c646b8328bb/venv/lib/python2.7/site-packages/ > >> Bio > >> biopython-1.62-py2.7.egg-info > >> BioSQL > >> docopt-0.6.1-py2.7.egg-info > >> docopt.py > >> docopt.pyc > >> easy-install.pth > >> Levenshtein.so > >> ngs > >> ngs_tools-0.1.6-py2.7.egg-info > >> pip-1.3.1-py2.7.egg > >> python_Levenshtein-0.10.2-py2.7.egg-info > >> setuptools-0.6c11-py2.7.egg > >> setuptools.pth > >> > >> Thanks, > >> Carlos > >> ___________________________________________________________ > >> Please keep all replies on the list by using "reply all" > >> in your mail client. To manage your subscriptions to this > >> and other Galaxy lists, please use the interface at: > >> http://lists.bx.psu.edu/ > >> > >> To search Galaxy mailing lists use the unified search at: > >> http://galaxyproject.org/search/mailinglists/ > > > > > > > > ___________________________________________________________ > > Please keep all replies on the list by using "reply all" > > in your mail client. To manage your subscriptions to this > > and other Galaxy lists, please use the interface at: > > http://lists.bx.psu.edu/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
