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.diehl@uni.lu<mailto:sarah.diehl@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. -----
?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-bounces@lists.galaxyproject.org> on behalf of Sarah DIEHL <sarah.diehl@uni.lu> Sent: 20 July 2016 09:51 To: 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.diehl@uni.lu<mailto:sarah.diehl@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. -----
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.diehl@uni.lu<mailto:sarah.diehl@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.vazov@usit.uio.no<mailto:n.a.vazov@usit.uio.no>> Date: Thursday 21 July 2016 09:36 To: Sarah DIEHL <sarah.diehl@uni.lu<mailto:sarah.diehl@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-bounces@lists.galaxyproject.org<mailto:galaxy-dev-bounces@lists.galaxyproject.org>> on behalf of Sarah DIEHL <sarah.diehl@uni.lu<mailto:sarah.diehl@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.diehl@uni.lu<mailto:sarah.diehl@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. -----
participants (2)
-
Nikolay Aleksandrov Vazov -
Sarah DIEHL