Hi Anna,

On Fri, Mar 27, 2015 at 10:39 AM Anna Terry <iseeglass@googlemail.com> wrote:
I'm still having major issues with repo updates.

1)
I'm getting this message for installing dependencies for package_samtools_1_1 that it says are missing:

Error installing tool dependency ncurses version 5.9: Unable to locate required tool shed repository named package_ncurses_5_9 owned by iuc with revision c0735727b530. Error installing tool dependency zlib version 1.2.8: Unable to locate required tool shed repository named package_zlib_1_2_8 owned by iuc with revision 03abe628fbe8.Installed tool dependencies: ncurses,zlib


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.
 
But I have these packages installed, which are the latest revisions.
package_ncurses_5_9
 iuc
package_zlib_1_2_8 iuc
 63a4a902cda2

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?
 
3)
Still getting:

Found

The resource was found at http://toolshed.g2.bx.psu.edu/repository/check_for_updates?galaxy_url=https://galaxy.hpc.qmul.ac.uk/&name=bam_to_sam&owner=devteam&changeset_revision=c09a20532957; you should be redirected automatically.

For any repository when I click on "Get repository updates".  I am not redirected automatically, clicking the link doesn't work, only pasting it into the browser bar.

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

Help would be greatly appreciated, as I'm thinking something major has gone wrong and that I will have to reinstall galaxy.

Many thanks

Anna


On 6 March 2015 at 16:50, Anna Terry <iseeglass@googlemail.com> wrote:
Hi,
I have a few installed tool shed repositories which are showing that updates are available.  When I click get repository updates, instead of the usual upate page, I get a page that simply says

This is for bam_to_sam, but same problem for blast_datatypes, pileup_interval and sam_to_bam too.

Anyone have any ideas why I'm seeing this?

Cheers

Anna

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