Re: [galaxy-dev] tool_dependencies.xml format

2013-09-17 Thread Bjoern Gruening
Hi James, thanks for your thoughts on abstraction of common tasks. For most of these things we have now patches in bitbucket. Similar recipes could be: autoconf: default to configure; make; make install, allow providing configuration options

Re: [galaxy-dev] tool_dependencies.xml format

2013-08-27 Thread Nate Coraor
On Aug 26, 2013, at 11:59 AM, James Taylor wrote: On Mon, Aug 26, 2013 at 11:48 AM, John Chilton chil...@msi.umn.edu wrote: I think it is interesting that there was push back on providing infrastructure (tool actions) for obtaining CBL from github and performing installs based on it because

Re: [galaxy-dev] tool_dependencies.xml format

2013-08-27 Thread John Chilton
Before I went on that tangent, I should have said I of course agree with 100% of what James said in the original e-mail on this thread. For what it is worth, I believe the higher-level constructs he outlined are essential to the long term adoption of the tool shed. On Tue, Aug 27, 2013 at 1:59

[galaxy-dev] tool_dependencies.xml format

2013-08-26 Thread James Taylor
All, I've been seeing some examples of tool_depedencies.xml come across of the list, and I'm wondering if there are ways that it can be simplified. When we were first defining these features, we talked about having high level recipes for certain types of installs. This could greatly simplify

Re: [galaxy-dev] tool_dependencies.xml format

2013-08-26 Thread John Chilton
James, et. al. I think it is interesting that there was push back on providing infrastructure (tool actions) for obtaining CBL from github and performing installs based on it because it was not in the tool shed and therefore less reproducible, but the team believes infrastructure should be put in

Re: [galaxy-dev] tool_dependencies.xml format

2013-08-26 Thread James Taylor
On Mon, Aug 26, 2013 at 11:48 AM, John Chilton chil...@msi.umn.edu wrote: I think it is interesting that there was push back on providing infrastructure (tool actions) for obtaining CBL from github and performing installs based on it because it was not in the tool shed and therefore less