On Wed, Dec 19, 2012 at 5:20 PM, David Gene Morgan <dagmorga@indiana.edu> wrote:

Hi,

I just installed a galaxy server and ran into something that may be a deliberate feature or a genuine bug when trying to install a package from the main tool shed. I got the Admin tab working, went to the section dealing with tool sheds and selected "Search for valid tools" in the Galaxy main too shed. I was able to find the tool I wanted (NCBI Blast+, and I found multiple revisions) but I never found anything remotely like an "Install" button. There are bare-bones instructions for a manual install of the tool, but nothing automatic.

However, if I start with "Browse valid repositories" and _then_ search for "ncbi blast" (and not "ncbi blast+"), I find a single revision that has a "Preview and install" option and an "Install into local Galaxy" button.

So the only question here is whether this behavior is a bug or a feature. In other words, should I be able to automatically install packages using my first approach, or does Galaxy prevent this deliberately?

As you noticed there is more than one repository offering an NCBI BLAST+ wrapper, perhaps only some of them are up to date enough to allow you to automatically 'install' it? Or there is a problem on others? The one you probably want is under the core team's account (due to it having previously been bundled with Galaxy itself), but I wrote it and have been updating it since. Another issue is which tool shed are you looking at (live or testing) and which version of Galaxy do you have (release or central, i.e. the stable releases or the in progress development version). Regards, Peter