[galaxy-dev] Galaxy News: GCCBOSC Training Topic Voting closes Wednesday!

[Dave Clements]

Hello all,

The February 2018 Galaxy News
 is out!

   - Events 
  - *GCCBOSC 2018 training topic voting ends tomorrow*
  

 - GCCBOSC Sponsorships
 
:
 highlighting *PeerJ
 * and call
 for sponsors
 
  - *Continental* community meetings in *Europe* (March, Freiburg)
  

   and *Africa* (April, Cape Town)
  

  - The Galaxy Administrators Course
  

   in Oslo is done, and training material and a preview of 18.01
  release from the course are now online.
   - Blog post: Galaxy R Markdown Tools
   

   - 111 new publications
   
   - Openings in 3 groups on 2 continents
   
   - Public Galaxy Server News
   
*(Hint: there are new servers.)*
   - ToolShed contributions
   
   - And other news
    too

See the full newsletter  for
all the news.
Dave C and the Galaxy Community

-- 
https://galaxyproject.org/
https://usegalaxy.org/
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[galaxy-dev] abnormal termination at worker using supervisord

[Vipin TS]

Dear developers,

We are experiencing a job dispatching issue on our public galaxy instance (
https://galaxy.inf.ethz.ch/). On the compute machine, I am not able to
start the workers. The following messages got from the worker log file:

migrate.versioning.repository DEBUG 2018-01-30 12:23:41,816 Repository
lib/galaxy/model/migrate loaded successfully

migrate.versioning.repository DEBUG 2018-01-30 12:23:41,816 Config:
OrderedDict([('db_settings', OrderedDict([('__name__', 'db_settings'),
('repository_id', 'Galaxy'), ('version_table', 'migrate_version'),
('required_dbs', '[]')]))])

After this line, it is restarting the process again and stop at the same
message.

I have checked the status of the workers through supervisor few times and
it exited.

-bash-4.2$ supervisorctl status

galaxy:worker0   STARTING


galaxy:worker0   BACKOFF   Exited too quickly (process log
may have details)


galaxy:worker0   FATAL Exited too quickly (process log
may have details)

my config/galaxy.ini

[server:worker0]

use  = egg:Paste#http

port = 

host = COMPUTE.MACHINE.IP

use_threadpool = true

threadpool_workers = 5

config/job_conf.xml



















1





config/galaxy_supervisor.conf

[program:galaxy_worker]

command = /tools/galaxy_ratschlab/.venv/bin/python
./lib/galaxy/main.py -c /tools/galaxy_ratschlab/config/galaxy.ini
--server-name=worker%(process_num)s
--log-file=/tools/galaxy_ratschlab/worker%(process_num)s.log

directory   = /tools/galaxy_ratschlab

process_name= worker%(process_num)s

numprocs= 2

umask   = 022

autostart   = true

autorestart = true

startsecs   = 20

user= galaxy

environment =
VIRTUAL_ENV="/tools/galaxy_ratschlab/.venv",PATH="/tools/galaxy_ratschlab/.venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin",PYTHONHOME="/tools/galaxy_ratschlab/.venv"

I tried to restart but didn't help, anything wrong with my configuration?
Please let me know what you think and need.

Thanks in advance!

Vipin
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Re: [galaxy-dev] Text file busy and conda

[Marius van den Beek]

Hi John,

when you say tool autoinstalled via conda do you mean that the dependencies
were automatically installed during the repository installation process,
or that you have `conda_auto_install = True` in your galaxy.ini ?

The latter is not working reliably while the dependencies have not finished
the installation process.
To avoid this you can make sure that the dependency is correctly installed
before running the tool
(the dependency in the admin panel -> Manage tool dependencies is green and
no conda process is still active).

Best,
Marius

On 30 January 2018 at 03:15, John Letaw  wrote:

> Hi all,
>
>
>
> I’m receiving the following error trying to access tools autoinstalled via
> conda:
>
>
>
> Fatal error: Exit code 126 ()
>
> ~/galaxy/database/jobs_directory/000/38/tool_script.sh: line 41:
> ~/galaxy/database/dependencies/_conda/envs/mulled-v1-
> bb83f93efd111e042823e53ddfa74c32d81ba74cceca9445dfddfc9e940ff738/bin/samtools:
> Text file busy
>
>
>
> So, something is happening too fast I guess, meaning a process is
> attempting access while this is being created.  Any ideas on how I can
> diagnose this?  Not seeing any other errors floating around the logs.
> Maybe we are dealing with a lustre file locking issue?
>
>
>
> Thanks,
>
> John
>
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