Hi Nikolay,

thanks a lot for the hint. I looked up the apache option and everywhere it says 
that something is wrong if you have to change that ;-). I did it anyway and I 
can see in the logs that a very long request appears that doesn't look right 
(see attached file) and afterwards I just get an empty page.

Best regards,
Sarah


----
Sarah Diehl
HPC System Administrator

UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
L-4371 Belvaux
T +352 46 66 44 5360
sarah.di...@uni.lu<mailto:sarah.di...@uni.lu>     
http://lcsb.uni.lu<http://lcsb.uni.lu/>
-----
This message is confidential and may contain privileged information. It is 
intended for the named recipient only. If you receive it in error please notify 
me and permanently delete the original message and any copies.
-----


From: Nikolay Aleksandrov Vazov 
<n.a.va...@usit.uio.no<mailto:n.a.va...@usit.uio.no>>
Date: Thursday 21 July 2016 09:36
To: Sarah DIEHL <sarah.di...@uni.lu<mailto:sarah.di...@uni.lu>>, 
"galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>" 
<galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>>
Subject: Re: errors when updating tools


​Hi, Sarah,


I can't be of much help on the tools issue but the "Request-URI Too Large" 
error can be fixed by adding a line like :


LimitRequestFieldSize 12392


(the size is a number of bytes which reflects the length of the uri eventually. 
For my setup, the above number does the job)


This line shall be added into your httpd.conf of ssl.conf in case you are using 
https connection. It shall be placed within


<VirtualHost *: ... >
        ​here

</VirtualHost>


Cheers


Nikolay

===============
Nikolay Vazov, PhD
Department for Research Computing, University of Oslo
________________________________
From: galaxy-dev 
<galaxy-dev-boun...@lists.galaxyproject.org<mailto:galaxy-dev-boun...@lists.galaxyproject.org>>
 on behalf of Sarah DIEHL <sarah.di...@uni.lu<mailto:sarah.di...@uni.lu>>
Sent: 20 July 2016 09:51
To: 
galaxy-dev@lists.galaxyproject.org<mailto:galaxy-dev@lists.galaxyproject.org>
Subject: [galaxy-dev] errors when updating tools

Hi,

I just updated our Galaxy from 15.10 to 16.04. I also wanted to update the 
tools installed, but I'm (again) getting a whole bunch of different errors.


Some of the updated tools rely on package_cairo_1_12_14, which fails, because 
it cannot find some of it's dependencies (see package_cairo_errors.jpg):

> Error installing tool dependency fontconfig version 2.11.1: Unable to locate 
> required tool shed repository named package_fontconfig_2_11_1 owned by iuc 
> with revision 2ce32675340e.
> Error installing tool dependency freetype version 2.5.2: Unable to locate 
> required tool shed repository named package_freetype_2_5_2 owned by iuc with 
> revision 3b09e7916896.

In the main overview of the repository I also see the message "Dependency was 
not resolved by any resolver module."  (see package_cairo_resolver.jpg). Is 
this related and something I should worry about? I did not touch the resolver 
configuration, I left the line in galaxy.ini commented.
I also don't understand why it tries to install a different revision of a 
package repo that's already installed. I'm having similar errors for some other 
packages.


Furthermore, when I try to "Get Updates" for cuffdiff, I get an internal server 
error (see cuffdiff_update_error.txt). The same for macs2 (see 
macs2_update_error.jpg).

When I try to install the newest version of cuffdiff from the toolshed, after I 
click "Install to Galaxy", I get a "Request-URI Too Large" error (from apache I 
guess). The last message before it fails in the Galaxy log is "Building 
repository dependency relationships...".


I'm a bit reluctant to update any package repositories I have installed, since 
in the past this lead to dependencies breaking. Also uninstalling and 
reinstalling usually doesn't help, since the database keeps the records and 
once it's messed up it stays messed up. I checked on the galaxy-stable docker 
image and there everything works fine, so I guess it's related to my Galaxy 
instance, not the package/tool repositories.

Any help on how to solve this is greatly appreciated!

Best regards,
Sarah


----
Sarah Diehl
HPC System Administrator

UNIVERSITÉ DU LUXEMBOURG

LUXEMBOURG CENTRE FOR SYSTEMS BIOMEDICINE
Campus Belval | Biotech II
6, avenue du Swing
L-4371 Belvaux
T +352 46 66 44 5360
sarah.di...@uni.lu<mailto:sarah.di...@uni.lu>     
http://lcsb.uni.lu<http://lcsb.uni.lu/>
-----
This message is confidential and may contain privileged information. It is 
intended for the named recipient only. If you receive it in error please notify 
me and permanently delete the original message and any copies.
-----

10.184.148.20 - - [21/Jul/2016:11:38:18 +0200] "GET 
/admin_toolshed/prepare_for_install?changeset_revisions=0f32ad418df8&repository_ids=497bb1cd1c72a204&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F
 HTTP/1.1" 200 - 
"https://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?repository_id=497bb1cd1c72a204&changeset_revision=0f32ad418df8";
 "Mozilla/5.0 (Macintosh; Intel Mac OS X 10.10; rv:47.0) Gecko/20100101 
Firefox/47.0"
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:39,783 Creating repository dependency objects...
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:45,586 Skipping installation of revision 0f32ad418df8 of 
repository 'cuffdiff' because it was installed with the (possibly updated) 
revision 5ce5197de50c and its current installation status is 'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:45,593 Skipping installation of revision 93cd8e03820c of 
repository 'package_pixman_0_32_4' because it was installed with the (possibly 
updated) revision 93cd8e03820c and its current installation status is 
'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:46,259 Skipping installation of revision 3de32cd300a9 of 
repository 'package_libpng_1_6_7' because it was installed with the (possibly 
updated) revision db14a391648d and its current installation status is 
'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:46,853 Skipping installation of revision 1e86d1cf79a4 of 
repository 'package_freetype_2_5_2' because it was installed with the (possibly 
updated) revision ee307f3ce5dc and its current installation status is 
'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:46,859 Skipping installation of revision 63a4a902cda2 of 
repository 'package_zlib_1_2_8' because it was installed with the (possibly 
updated) revision 63a4a902cda2 and its current installation status is 
'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:47,476 Skipping installation of revision 588666932a32 of 
repository 'package_libpng_1_6_7' because it was installed with the (possibly 
updated) revision 05df724aefbb and its current installation status is 
'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:48,106 Skipping installation of revision d88d844df0cb of 
repository 'package_fontconfig_2_11_1' because it was installed with the 
(possibly updated) revision b20e4c53891e and its current installation status is 
'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:48,723 Skipping installation of revision 45b16a3ab504 of 
repository 'package_libxml2_2_9_1' because it was installed with the (possibly 
updated) revision e5475acebd6e and its current installation status is 
'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:48,729 Skipping installation of revision 0d934b13250c of 
repository 'package_libcurl_7_35' because it was installed with the (possibly 
updated) revision 0d934b13250c and its current installation status is 
'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:48,734 Skipping installation of revision a65217367e4a of 
repository 'package_freetype_2_5_2' because it was installed with the (possibly 
updated) revision a65217367e4a and its current installation status is 
'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:48,740 Skipping installation of revision cd2ed5717e38 of 
repository 'package_cairo_1_12_14' because it was installed with the (possibly 
updated) revision cd2ed5717e38 and its current installation status is 
'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:48,745 Skipping installation of revision 899067a260d1 of 
repository 'package_cufflinks_2_2_1' because it was installed with the 
(possibly updated) revision 899067a260d1 and its current installation status is 
'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:49,404 Skipping installation of revision 754912f24120 of 
repository 'package_cummerbund_2_8_2' because it was installed with the 
(possibly updated) revision 13c270433440 and its current installation status is 
'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:49,410 Skipping installation of revision 52d6f646b3b5 of 
repository 'package_readline_6_2' because it was installed with the (possibly 
updated) revision 52d6f646b3b5 and its current installation status is 
'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:49,975 Skipping installation of revision 335ebf512407 of 
repository 'package_ncurses_5_9' because it was installed with the (possibly 
updated) revision 5e1760c773ba and its current installation status is 
'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:50,612 Skipping installation of revision 4d2fd1413b56 of 
repository 'package_r_3_1_2' because it was installed with the (possibly 
updated) revision 9f2fddb9d6e2 and its current installation status is 
'Installed'.
tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager 
DEBUG 2016-07-21 11:38:50,613 Building repository dependency relationships...
10.184.148.20 - - [21/Jul/2016:11:38:39 +0200] "POST 
/admin_toolshed/prepare_for_install HTTP/1.1" 302 - 
"https://galaxy-server.uni.lu/admin_toolshed/prepare_for_install?changeset_revisions=0f32ad418df8&repository_ids=497bb1cd1c72a204&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F";
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Firefox/47.0"
10.184.148.20 - - [21/Jul/2016:11:39:19 +0200] "GET 
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 HTTP/1.1" 200 - 
"https://galaxy-server.uni.lu/admin_toolshed/prepare_for_install?changeset_revisions=0f32ad418df8&repository_ids=497bb1cd1c72a204&tool_shed_url=https%3A%2F%2Ftoolshed.g2.bx.psu.edu%2F";
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Firefox/47.0"
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