Error while installing tool via Admin GUI: log?

Question: Error while installing tool via Admin GUI: log?

2.6 years ago by

Dear all, I am experiencing some troubles during the installation of tools via Admin GUI. I followed these tutorials: https://wiki.galaxyproject.org/Admin/GetGalaxy https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy I modified config/galaxy.ini according to the tutorials, and restarted the server via run.sh. Then I tried to install BWA via admin GUI but it returns errors. It fails during the installation process. The problem is that Galaxy doesn't return the installation error so that I don't understand what is the problem. Could someone please tell me where I can find the complete log? Also the View Tool Error Logs link in the interface is empty.

Thanks for the support,

Stefania

ADD COMMENT • link •

modified 2.6 years ago by Martin Čech ♦♦ 4.9k • written 2.6 years ago by merella.stefania • 0

2.6 years ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

Hello Stefania,

you should be able to see the error if you explore the admin interface a bit. Try Admin/Manage installed tools and then find bwa (it should be in the error state) click on it and you will see what went wrong. Whether it was a dependency or something else you should be able to click through and see the log.

ADD COMMENT • link written 2.6 years ago by Martin Čech ♦♦ 4.9k

Hi Martin, thanks for the answer. The problem is that in the error interface is not reported the error. BWA is in error state but then, if I click on it, the error page doesn't report the error. I posted the screen shot of the page. error_page Thanks,

Stefania

ADD REPLY • link written 2.6 years ago by merella.stefania • 0

Try the 'reset to install' as recommended by the error message. I would also try uninstalling fully and retrying again.

ADD REPLY • link written 2.6 years ago by Martin Čech ♦♦ 4.9k

I tried both, many times, but no one of those worked... Going back to my original question, is there a complete galaxy log where I can monitor what is going on during the installation? It seems that something is missed in the configuration but I can't understand what is, I followed the tutorials...

many many thanks for the support

Stefania

ADD REPLY • link written 2.6 years ago by merella.stefania • 0

Galaxy logs to the shell from which it is run unless you change it. How do you run Galaxy?

ADD REPLY • link written 2.6 years ago by Martin Čech ♦♦ 4.9k

Hi Martin, sorry for my late answer, I was not able to use computer and internet for a while.... I run galaxy in daemon mode. I use run.sh start/stop.. in the shell are not printed any messages... Is there a way to change it? Thanks

ADD REPLY • link written 2.6 years ago by merella.stefania • 0

Hi Martin, I think I found the error :) I had a look at run.sh script and I found that I can specify a log file in this way

sh run.sh --daemon --log-file=test_running.log

looking then at test_running.log I found out this line:

tool_shed.util.hg_util DEBUG 2016-04-19 11:19:52,220 Error cloning repository: [Errno 13] Permission denied: '/usr/local/src/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc'

The user that is running galaxy via web interface has no permissions to modify the folder needed to install tools :) It was a really easy problem... Sorry to have bothered all of you.. And many many thanks for the great help!!

Stefania

ADD REPLY • link written 2.6 years ago by merella.stefania • 0

Awesome, I am glad you solved it, goodjob! Thank you for using Galaxy also. :)

ADD REPLY • link written 2.6 years ago by Martin Čech ♦♦ 4.9k

Similar posts • Search »