On Tue, Apr 16, 2013 at 2:46 PM, John Chilton <chil...@msi.umn.edu> wrote: > Stepping back a little, is the right way to address Python > dependencies?
Looks like I missed this thread, hence: http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014169.html > I was a big advocate for inter-repository dependencies, > but I think taking it to the level of individual python packages might > be going too far - my thought was they were needed for big 100Mb > programs and stuff like that. It should work but it is a lot of boilerplate for something which should be more automated. > At the Java jar/Python library/Ruby gem > level I think using some of the platform specific packaging stuff to > creating isolated environments for each program might be a better way > to go. I agree, the best way forward isn't obvious here, and it may make sense to have tailored solutions for Python, Perl, Java, R, Ruby, etc packages rather than the current Tool Shed package solution. I've like to be able to just continue to write this kind of thing in my tool XML files and have it actually taken care of (rather than ignored): <requirements> <requirement type="python-module">numpy</requirement> <requirement type="python-module">Bio</requirement> </requirements> Adding a version key would be sensible, handling min/max etc as per Python packaging norms. Peter ___________________________________________________________ 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/