Hi Martin,  thanks for looking at this

On 27 March 2015 at 14:51, Martin Čech <marten@bx.psu.edu> wrote:

The requested revisions are from the Test Tool Shed, which means your package_samtools_1_1 is also installed from the Test Tool Shed. Please install only from the Main Tool Shed (https://toolshed.g2.bx.psu.edu) unless you want to test.

 

Great, thanks! It's now sorted.

 

2)
bam_to_sam has a red arrow icon indicating a newer installable revision is available, but when I check for updates it says:

The installed repository named 'bam_to_sam' is current, there are no updates available.

There are no newer entries for this on the Installed tool shed repositories page, just the one saying there is a newer revision.

Which Tool Shed is the tool installed from and what revision do you have?

 

Tool shed: toolshed.g2.bx.psu.edu
Revision: c09a20532957

3)

I think this has to do with your proxy configuration that is not following Tool Shed redirects properly.

 

Are you able to help me troubleshoot this?  Which bits of config files would help?

 

Many thanks

Anna