problem with revision updates for repositories.

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problem with revision updates for repositories.

Anna Terry
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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Re: problem with revision updates for repositories.

Anna Terry
Hi, can anyone help with this? TIA

On 6 March 2015 at 16:50, Anna Terry <[hidden email]> 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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Re: problem with revision updates for repositories.

Martin Čech
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? 

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

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? 

thanks

Martin

On Thu, Mar 12, 2015 at 10:37 AM Anna Terry <[hidden email]> wrote:
Hi, can anyone help with this? TIA

On 6 March 2015 at 16:50, Anna Terry <[hidden email]> 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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Re: problem with revision updates for repositories.

Anna Terry
Hi Martin,

On 12 March 2015 at 14:50, Martin Čech <[hidden email]> 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 <[hidden email]> wrote:
Hi, can anyone help with this? TIA

On 6 March 2015 at 16:50, Anna Terry <[hidden email]> 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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Re: problem with revision updates for repositories.

Anna Terry
In reply to this post by Anna Terry
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

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.

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.

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 <[hidden email]> 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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Re: problem with revision updates for repositories.

Martin Čech
Hi Anna,

On Fri, Mar 27, 2015 at 10:39 AM Anna Terry <[hidden email]> 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 <[hidden email]> 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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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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Re: problem with revision updates for repositories.

Anna Terry
Hi Martin,  thanks for looking at this

On 27 March 2015 at 14:51, Martin Čech <[hidden email]> 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?
 

toolshed.g2.bx.psu.edu
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

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Re: problem with revision updates for repositories.

Martin Čech


On Fri, Mar 27, 2015 at 11:10 AM Anna Terry <[hidden email]> wrote:
Hi Martin,  thanks for looking at this

On 27 March 2015 at 14:51, Martin Čech <[hidden email]> 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?
 

toolshed.g2.bx.psu.edu
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

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Re: problem with revision updates for repositories.

Anna Terry
Thanks Martin

On 27 March 2015 at 15:20, Martin Čech <[hidden email]> wrote:

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


Great, also sorted.

 

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.
 

Basically we are using apache as a proxy to serve galaxy on https.
Anyone able to help?


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Re: problem with revision updates for repositories.

Anna Terry
In reply to this post by Anna Terry
I've finally sorted this.  Here is my solution in case anyone else is getting stuck with this.
The URLs to the tool sheds in the file tool_sheds_conf.xml were http not https.
Changing them to https and restarting galaxy seems to have resolved this issue.
Anna


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