Hi Martin, On 12 March 2015 at 14:50, Martin Čech <marten@bx.psu.edu> wrote:

Hello Anna,

I was not able to replicate this issue. Can you please elaborate a little bit more on the setup your Galaxy has? Do you use proxy?

yes - could it be a problem with config here?

After clicking the URL you sent I will get redirected properly, can you please try visiting the url to check whether you get redirected?

clicking the link does nothing, but copying and pasting to nav bar works (but lose galaxy frame). The update then succeeds

If I understand it correctly for tools other than the mentioned ones the update feature works well for you, am I right? Are the working ones installed from the same toolshed?

All the updates that were available had this problem. If i click "get repository updates" for any repository (where no update is indicated as being available) I get the same problem, so I don't think its to do with what toolshed they are from - they are mostly the main toolshed anyway. Kind regards Anna

thanks

Martin

On Thu, Mar 12, 2015 at 10:37 AM Anna Terry <iseeglass@googlemail.com> wrote:

...

Hi, can anyone help with this? TIA

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 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=250151b4d934; you should be redirected automatically.

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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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 5e1760c773ba 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 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=250151b4d934; you should be redirected automatically.

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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On Fri, Mar 27, 2015 at 11:10 AM Anna Terry <iseeglass@googlemail.com> wrote:

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

This is one installable revision behind. Try selecting 'install latest revision' instead of updating in the repository dropdown.

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?

I am afraid I am not able to. But if you describe your proxy settings maybe somebody else will chime in.

Many thanks Anna