Re: [galaxy-dev] no universe_wsgi.ini & can't install tools from the standard toolshed because: "Initializing repository installation failed"
Thanks for the screenshot. That page will often and regrettably report errors when there are none. I think the advice I have been given by people who know the tool shed better is to click install and then leave that page and go to the list of installed repositories to track progress. Did that samtools install ever land up working? Usually if there is a problem with the installation the logs will be a little more clear that there is a problem. -John On Tue, Oct 7, 2014 at 4:51 PM, Chris Dagdigian wrote: > > > Martin Čech wrote: >> (2) There might have been some changes to the conf syntax regarding the >> dependency directory etc. since the version of universe.wsgi.ini that >> you are using. So please make sure you are using the current galaxy.ini >> file and try installing a tool again. If it does not go well please >> include the log of errors. >> > > Still seeing mysterious tool shed installation failures on brand new > servers running the stable checkout. > > After changing to HTTPS in tool_sheds_conf.xml I made much more progress > but for a few basic tools I get the web UI stuck on "installing > dependencies", no obvious error output and a javascript error about the > "initializing repository installation failed" when I navigate away. > > Screenshot showing what happens with samtools_0_1_18 attached. > > And the server logs don't show anything obvious going wrong: > >> 50.247.195.121 - - [07/Oct/2014:20:45:41 +] "POST >> /admin_toolshed/prepare_for_install HTTP/1.1" 200 - >> "http://54.165.218.123:8080/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=5a9571a9ebd4ce0a&changeset_revisions=171cd8bc208d"; >> "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, >> like Gecko) Chrome/37.0.2062.124 Safari/537.36" >> tool_shed.util.tool_dependency_util DEBUG 2014-10-07 20:45:43,539 Updating >> an existing record for version 0.1.18 of tool dependency samtools for >> revision 171cd8bc208d of repository package_samtools_0_1_18 by updating the >> status from Never installed to Installing. >> tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG >> 2014-10-07 20:45:43,563 Attempting to download via url: >> http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz >> 50.247.195.121 - - [07/Oct/2014:20:45:45 +] "POST >> /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - >> "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 >> (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) >> Chrome/37.0.2062.124 Safari/537.36" >> 50.247.195.121 - - [07/Oct/2014:20:45:48 +] "POST >> /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - >> "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 >> (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) >> Chrome/37.0.2062.124 Safari/537.36" >> 50.247.195.121 - - [07/Oct/2014:20:45:51 +] "POST >> /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - >> "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 >> (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) >> Chrome/37.0.2062.124 Safari/537.36" >> 50.247.195.121 - - [07/Oct/2014:20:45:54 +] "POST >> /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - >> "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 >> (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) >> Chrome/37.0.2062.124 Safari/537.36" >> 50.247.195.121 - - [07/Oct/2014:20:45:57 +] "POST >> /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - >> "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 >> (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) >> Chrome/37.0.2062.124 Safari/537.36" >> 50.247.195.121 - - [07/Oct/2014:20:46:00 +] "POST >> /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - >> "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 >> (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) >> Chrome/37.0.2062.124 Safari/537.36" >> 50.247.195.121 - - [07/Oct/2014:20:46:03 +] "POST >> /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - >> "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 >> (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) >> Chrome/37.0.2062.124 Safari/537.36" >> 50.247.195.121 - - [07/Oct/2014:20:46:06 +] "POST >> /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - >> "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 >> (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) >> Chrome/37.0.2062.124 Safari/537.36" >> 50.247.1
Re: [galaxy-dev] no universe_wsgi.ini & can't install tools from the standard toolshed because: "Initializing repository installation failed"
Martin Čech wrote: > (2) There might have been some changes to the conf syntax regarding the > dependency directory etc. since the version of universe.wsgi.ini that > you are using. So please make sure you are using the current galaxy.ini > file and try installing a tool again. If it does not go well please > include the log of errors. > Still seeing mysterious tool shed installation failures on brand new servers running the stable checkout. After changing to HTTPS in tool_sheds_conf.xml I made much more progress but for a few basic tools I get the web UI stuck on "installing dependencies", no obvious error output and a javascript error about the "initializing repository installation failed" when I navigate away. Screenshot showing what happens with samtools_0_1_18 attached. And the server logs don't show anything obvious going wrong: > 50.247.195.121 - - [07/Oct/2014:20:45:41 +] "POST > /admin_toolshed/prepare_for_install HTTP/1.1" 200 - > "http://54.165.218.123:8080/admin_toolshed/prepare_for_install?tool_shed_url=https://toolshed.g2.bx.psu.edu/&repository_ids=5a9571a9ebd4ce0a&changeset_revisions=171cd8bc208d"; > "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, > like Gecko) Chrome/37.0.2062.124 Safari/537.36" > tool_shed.util.tool_dependency_util DEBUG 2014-10-07 20:45:43,539 Updating an > existing record for version 0.1.18 of tool dependency samtools for revision > 171cd8bc208d of repository package_samtools_0_1_18 by updating the status > from Never installed to Installing. > tool_shed.galaxy_install.tool_dependencies.recipe.step_handler DEBUG > 2014-10-07 20:45:43,563 Attempting to download via url: > http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.18-linux-x86_64.tgz > 50.247.195.121 - - [07/Oct/2014:20:45:45 +] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/37.0.2062.124 Safari/537.36" > 50.247.195.121 - - [07/Oct/2014:20:45:48 +] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/37.0.2062.124 Safari/537.36" > 50.247.195.121 - - [07/Oct/2014:20:45:51 +] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/37.0.2062.124 Safari/537.36" > 50.247.195.121 - - [07/Oct/2014:20:45:54 +] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/37.0.2062.124 Safari/537.36" > 50.247.195.121 - - [07/Oct/2014:20:45:57 +] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/37.0.2062.124 Safari/537.36" > 50.247.195.121 - - [07/Oct/2014:20:46:00 +] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/37.0.2062.124 Safari/537.36" > 50.247.195.121 - - [07/Oct/2014:20:46:03 +] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/37.0.2062.124 Safari/537.36" > 50.247.195.121 - - [07/Oct/2014:20:46:06 +] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/37.0.2062.124 Safari/537.36" > 50.247.195.121 - - [07/Oct/2014:20:46:09 +] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, like Gecko) > Chrome/37.0.2062.124 Safari/537.36" > 50.247.195.121 - - [07/Oct/2014:20:46:13 +] "POST > /admin_toolshed/repository_installation_status_updates HTTP/1.1" 200 - > "http://54.165.218.123:8080/admin_toolshed/prepare_for_install"; "Mozilla/5.0 > (Macintosh; Intel Mac OS X 10_8_5) AppleWebKit/537.36 (KHTML, lik
Re: [galaxy-dev] no universe_wsgi.ini & can't install tools from the standard toolshed because: "Initializing repository installation failed"
Thanks for the rapid reply! Right now I'm thinking that my toolshed issues are caused by the HTTP to HTTPS redirects on the main tool shed servers. I've set the URL to use https in the tool_sheds_conf.xml page and we'll see how far I can get ... Regards, Chris Martin Čech wrote: > Hi Chris, > > (1) Galaxy configuration has been moved to /config/galaxy.ini > (https://bitbucket.org/galaxy/galaxy-dist/src/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb/config/) > > (2) There might have been some changes to the conf syntax regarding the > dependency directory etc. since the version of universe.wsgi.ini that > you are using. So please make sure you are using the current galaxy.ini > file and try installing a tool again. If it does not go well please > include the log of errors. > > Let us know how it goes. > > Thanks > > Martin ___ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] no universe_wsgi.ini & can't install tools from the standard toolshed because: "Initializing repository installation failed"
Hi Chris,
(1) Galaxy configuration has been moved to /config/galaxy.ini
(
https://bitbucket.org/galaxy/galaxy-dist/src/579d211c2b0fa8ef4195930cb999edbb9a0cf8eb/config/
)
(2) There might have been some changes to the conf syntax regarding the
dependency directory etc. since the version of universe.wsgi.ini that you
are using. So please make sure you are using the current galaxy.ini file
and try installing a tool again. If it does not go well please include the
log of errors.
Let us know how it goes.
Thanks
Martin
On Tue, Oct 7, 2014 at 3:50 PM, Chris Dagdigian wrote:
>
> Hi folks,
>
> Got a strange problem - it's hit me on all my self-install options today
> including using the Chef cookbook as well as the galaxy mecurial install
> method on Ubuntu 12.04 LTS
>
> I'm trying to build a local galaxy that supports a few common extra
> tools (things like samtools etc.)
>
> I can boot a fresh Ubuntu 12.04 LTS and follow the instructions at
> getgalaxy.org:
>
> > hg clone https://bitbucket.org/galaxy/galaxy-dist/
> > cd galaxy-dist
> > hg update stable
> sh ./run.sh
>
>
> There are two strange things that don't quite match what I'm expecting
> to see from the docs ...
>
> (1) The file "universe_wsgi.ini " no longer gets created in
> galaxy-dist/ after running "run.sh" for the first time. This is strange
> because I remember it working days ago but now on fresh server and fresh
> checkout the file does not get created and I have to manually create one
> in oder to set "host = 0.0.0.0"
>
> (2) I can't even install simple tools like samtools from the standard
> tool sheds. The status page gets stuck at "installing dependencies" and
> if I navigate away I get a browser javascript error ("Initializing
> repository installation failed"
>
> Any tips or tricks appreciated, thanks!
>
> Regards,
> Chris
>
>
>
>
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client. To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> http://lists.bx.psu.edu/
>
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/mailinglists/
>
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
[galaxy-dev] no universe_wsgi.ini & can't install tools from the standard toolshed because: "Initializing repository installation failed"
Hi folks,
Got a strange problem - it's hit me on all my self-install options today
including using the Chef cookbook as well as the galaxy mecurial install
method on Ubuntu 12.04 LTS
I'm trying to build a local galaxy that supports a few common extra
tools (things like samtools etc.)
I can boot a fresh Ubuntu 12.04 LTS and follow the instructions at
getgalaxy.org:
> hg clone https://bitbucket.org/galaxy/galaxy-dist/
> cd galaxy-dist
> hg update stable
sh ./run.sh
There are two strange things that don't quite match what I'm expecting
to see from the docs ...
(1) The file "universe_wsgi.ini " no longer gets created in
galaxy-dist/ after running "run.sh" for the first time. This is strange
because I remember it working days ago but now on fresh server and fresh
checkout the file does not get created and I have to manually create one
in oder to set "host = 0.0.0.0"
(2) I can't even install simple tools like samtools from the standard
tool sheds. The status page gets stuck at "installing dependencies" and
if I navigate away I get a browser javascript error ("Initializing
repository installation failed"
Any tips or tricks appreciated, thanks!
Regards,
Chris
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
