Question: Error while installing tool via Admin GUI: log?
0
gravatar for merella.stefania
2.6 years ago by
merella.stefania0 wrote:

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 COMMENTlink modified 2.6 years ago by Martin Čech ♦♦ 4.9k • written 2.6 years ago by merella.stefania0
1
gravatar for Martin Čech
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 COMMENTlink 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 REPLYlink written 2.6 years ago by merella.stefania0

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

ADD REPLYlink 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 REPLYlink written 2.6 years ago by merella.stefania0

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

ADD REPLYlink 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 REPLYlink written 2.6 years ago by merella.stefania0

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 REPLYlink written 2.6 years ago by merella.stefania0

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

ADD REPLYlink written 2.6 years ago by Martin Čech ♦♦ 4.9k
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