Galaxy Interactive Tools - linked to wrong port
by Doris Brockmann
Hi,
I installed Galaxy on an Ubuntu (18.04) VM following the 'Galaxy
Installation with Ansible' tutorial. Galaxy is serving on localhost and
does not use SSL.
I then followed the 'Galaxy Interactive Tools' tutorial to
install/enable Interactive Tools.
I skipped the part 'Getting a wildcard SSL certificate' and I modified
the group variables file group_vars/galayservers.yml as follows
nginx_servers:
- galaxy # NOT redirect-ssl
- galaxy-gie-proxy
instead of
nginx_ssl_servers:
- galaxy
- galaxy-gie-proxy
and in the templates/nginx/galaxy-gie-proxy.j2 file, I changed
server {
# Listen on port 443
listen *:443 ssl;
to
server {
# Listen on port 80 (no SSL)
listen *:80;
When I execute EtherCalc (or RStudio), the link given in the blue box
under 'click here to display' is something like this:
http://4b187121143038ff-e0f2473dafce49c98787ab723e8a39b1.interactivetoole...
but the actual view is found here (modification by hand):
http://4b187121143038ff-e0f2473dafce49c98787ab723e8a39b1.interactivetoole...
It seems that the Interactive Tools Proxy serves on the wrong port.
The gie_proxy_port is 8000 and the proxy_pass in
/etc/nginx/sites-enabled/galaxy-gie-proxy is http://localhost:8000
Does anyone have an idea how to solve the problem?
Thanks in advance,
Doris
--
Doris BROCKMANN
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Portable : +33 (0)6 03 18 97 76
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SIRET : 433 960 762 00030 – APE 671 C – TVA FR 96 433 960 762/
2 years, 4 months
To implement a one-click test for a Galaxy tool.
by Jin Li
Hi all,
We have a tool in Galaxy at https://usegalaxy.eu/root?tool_id=moabs.
We want to implement a one-click test using small data so that users
can quickly understand how to use the interface. There are two
difficulties in implementing the one-click test.
1. How to store small test data so that every new user can access it?
2. How to configure program settings automatically for the test data?
so that the test data is automatically uploaded, and other parameters
are pre-configured.
Please help suggest any possible solution to a one-click test. Thank you.
Best regards,
Jin
2 years, 4 months
How to earn money online
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2 years, 4 months
***UNCHECKED*** A couple of BCC2020 Deadlines are today
by Dave Clements
Hi all,
Just a reminder that there are a couple of BCC2020 (BOSC + Galaxy)
deadlines today, July 10:
1. Birds of a feather submissions: https://bit.ly/bcc-propose-a-bof
If you are attending the meeting part of BCC, and you would benefit from
gathering your community at a BoF then please submit a proposal.
We also need these. Right now we have lots of attendees, and very few BoFs
(https://bcc2020.sched.com/overview/subject/BoF). This combination may not
work well in an online setting.
We might also extend the deadline to Sunday night. However, we might not.
So if you see this today, then please submit in the next ~12 or so hours.
2. Early registration closes: https://bcc2020.github.io/Registration/
At US Pacific time. (about 13:45 from right now). Registration rates
double after that, although they still aren't expensive. However, this
event might sell out before the end of the day. So, might want to register
now....
Thanks everyone,
Dave C
--
https://galaxyproject.org/
2 years, 4 months
***UNCHECKED*** Nextflow within galaxy
by Luc Cornet
Hi everyone,
I would like to run a Netxflow script in galaxy (yes I know it’s strange).
So I made a test but I have a problem that I don’t undertstand, I am able to launch my Nextflow tool in galaxy but not to complete the analysis.
The log out of galaxy :
> juil.-07 19:28:53.888 [main] DEBUG nextflow.Session - Work-dir: /Users/luc/Documents/Programs/galaxy/database/jobs_directory/000/24/working/work [Mac OS X]
juil.-07 19:28:53.888 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/luc/Documents/Programs/galaxy/tools/BCCM-tools/bin
juil.-07 19:28:53.988 [main] DEBUG nextflow.Session - Session start invoked
juil.-07 19:28:54.296 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
juil.-07 19:28:54.368 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
juil.-07 19:28:54.368 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
juil.-07 19:28:54.372 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
juil.-07 19:28:54.375 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=4; memory=16 GB; capacity=4; pollInterval=100ms; dumpInterval=5m
juil.-07 19:28:54.446 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Testo -- maxForks: 4
juil.-07 19:28:54.477 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
juil.-07 19:28:54.477 [main] DEBUG nextflow.Session - Session await
juil.-07 19:28:54.579 [Task submitter] DEBUG nextflow.executor.LocalTaskHandler - Launch cmd line: /bin/bash -ue .command.run
juil.-07 19:28:54.584 [Task submitter] INFO nextflow.Session - [37/23b693] Submitted process > Testo
juil.-07 19:28:54.647 [Task monitor] DEBUG n.processor.TaskPollingMonitor - Task completed > TaskHandler[id: 1; name: Testo; status: COMPLETED; exit: 0; error: -; workDir: /Users/luc/Documents/Programs/galaxy/database/jobs_directory/000/24/working/work/37/23b693d7b8dbbf227f19b3dd9780a7]
juil.-07 19:28:54.674 [main] DEBUG nextflow.Session - Session await > all process finished
juil.-07 19:28:54.675 [main] DEBUG nextflow.Session - Session await > all barriers passed
juil.-07 19:28:54.682 [main] DEBUG nextflow.trace.StatsObserver - Workflow completed > WorkflowStats[succeedCount=1; failedCount=0; ignoredCount=0; cachedCount=0; succeedDuration=6ms; failedDuration=0ms; cachedDuration=0ms]
juil.-07 19:28:54.855 [main] DEBUG nextflow.CacheDB - Closing CacheDB done
juil.-07 19:28:54.869 [main] DEBUG nextflow.script.ScriptRunner - > Execution complete -- Goodbye
And the log in galaxy:
> juil.-08 11:38:09.834 [main] DEBUG nextflow.Session - Work-dir: /Users/luc/Documents/Programs/galaxy/database/jobs_directory/000/27/working/work [Mac OS X]
juil.-08 11:38:09.834 [main] DEBUG nextflow.Session - Script base path does not exist or is not a directory: /Users/luc/Documents/Programs/galaxy/tools/BCCM-tools/bin
juil.-08 11:38:10.001 [main] DEBUG nextflow.Session - Session start invoked
juil.-08 11:38:10.373 [main] DEBUG nextflow.script.ScriptRunner - > Launching execution
juil.-08 11:38:10.450 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: null
juil.-08 11:38:10.450 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'local'
juil.-08 11:38:10.455 [main] DEBUG nextflow.executor.Executor - [warm up] executor > local
juil.-08 11:38:10.458 [main] DEBUG n.processor.LocalPollingMonitor - Creating local task monitor for executor 'local' > cpus=4; memory=16 GB; capacity=4; pollInterval=100ms; dumpInterval=5m
juil.-08 11:38:10.534 [main] DEBUG nextflow.processor.TaskProcessor - Creating operator > Testo -- maxForks: 4
juil.-08 11:38:10.591 [main] DEBUG nextflow.script.ScriptRunner - > Await termination
Can someone help me with this ?
Best,
Luc
------------
Luc Cornet, PhD
Bio-informatician
Mycology and Aerobiology
Sciensano
2 years, 4 months
