Hello Ira,

Thanks for all of the work you've been doing n your repositories - I've been 
getting email updates from your repository changes.

I'm not quite sure what is causing this behavior.  I've taken a glance at your 
many dependency definitions, and they look correct, so I'm not seeing why 
certain directory paths are required by some repositories.  Required paths like 
this are handled with complex repository dependencies (which you have correctly 
defined), so you may have uncovered a corner-case issue that I didn't encounter 
during development.

This may take a bit of time to figure out and resolve, but I'll let you know as 
soon as we uncover and resolve the problem.


Greg Von Kuster

On Mar 5, 2013, at 1:49 AM, Ira Cooke wrote:

> Hi, 
> I've just uploaded a set of updates to my proteomics tools on the toolshed.  
> These contain my best attempt to implement automatic dependency installation 
> ... and for the most part it seems to work. 
> I have encountered the following issues though
> (1) I don't see any way to ensure that one repository_dependency is installed 
> before all others.  In my case this is important because I have an installer 
> package (galaxy_protk) which needs to be installed before other package 
> installs will work.
> For example .. try installing
> http://toolshed.g2.bx.psu.edu/view/iracooke/omssa
> (2) Running multiple repo installs at once is not reliable (sorry this is so 
> vague).  When I have many dependencies being installed at once I get the 
> following error (for example)
> "Could not cd to 
> ./database/tmp/tmpbIqBW8/galaxy_protk/./database/tmp/tmp3vhKn6/galaxy_protk"
> It looks like a path is not being constructed correctly. 
> If I wait until the currently installed repo is finished .. then try 
> uninstalling and reinstalling it works.
> Sorry this is vague but if you try installing any of the following 
> repositories you should see what I mean
> http://toolshed.g2.bx.psu.edu/view/iracooke/xtandem
> http://toolshed.g2.bx.psu.edu/view/iracooke/msgfplus
> http://toolshed.g2.bx.psu.edu/view/iracooke/tpp_prophets
> Anyway .. and just so it doesn't just sound like I'm complaining ... I think 
> the dependency installation stuff is hugely useful.  It took me a while to 
> figure out all the details .. but I think it makes sense now.
> Cheers
> Ira
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