Cloudman - using different worker instance types
by David Kovalic
Hi,
I want to be able to use different AWS worker instance types than are
currently provided in the cloudman "Add worker nodes" menu.
Say for example I am interested in using AWS 'r3.*' instance types as my
workers, how can I add these to be available in the cloudman interface?
Thanks,
David
6 years
Adding categories to Main
by Keith Suderman
Dear Galaxy Team,
A colleague would like to upload some NLP (Natural Language Processing) tools to the Galaxy Test/Main tools sheds, but we are unclear what "categories" to use for the tools. I see that the Main/Test tools sheds have a category for "Text Manipulation", but that does not seem appropriate for NLP tools. Is it possible to have new categories added to the tool shed(s)? If so, what is the process?
I am just starting to investigate setting up our own local tool shed and I am coming across mentions of repository capsules and exporting tool sheds. Would it be preferable to install the NLP tools to a local tool shed and then export a repository/capsule to be imported to the Test/Main tools sheds? What happens if our tool shed uses a disjoint set of categories than Test/Main?
Cheers,
Keith
------------------------------
Research Associate
Department of Computer Science
Vassar College
Poughkeepsie, NY
6 years
custom tool - accessing user's data in bash script
by Piotr Grabowski
Hello Galaxy Devs and Deployers!
I have a rather basic question about how to handle custom tools in Galaxy
(I'm fresh to this framework). I am trying to link my local Galaxy with
KNIME workflow that we developed in our group. I am trying to link it via a
bash script that is running headless KNIME and it seems almost to work,
but...
In order for this workflow to run I have to specify in the command line
things like result folder or where a dynamically generated parameter file
is located.
This parameter file is generate by the bash script before running KNIME.
The paths will be always dynamic, depending on users etc. So I can't simply
hard-code the path. Is there a way to make bash aware of where the current
Galaxy user's folders and files are upon execution in Galaxy?
Below a simplified scheme of what I am doing:
User uploads txt file -> Clicks RUN -> bash script builds a parameter file
(gawk ... >> param.csv) -> /knime run workflow --set the path to the
parameter .csv file + set export folder
Any ideas ?
Best,
Piotr
6 years
LDAP and valid username
by Edouard Hirchaud
Hi,
I configure authentication with the LDAP (Active Directory) of my
compagny. But the username (sAMAccoutName) contains a dot (eg :
e.hirchaud).
And that was a problem because the dot is not allow in galaxy username
and auto-registration fails because of that.
For testing I change the regex in "security/validate_user_input.py" and
authorize character dot and it's work !
I know its not a good practice to change core code so I want to know
if they are known "risks" or sides effects if I keep this change and if
you have a best solution ?
Thanks!
Edouard
--
Édouard Hirchaud
ANSES
Laboratoire de Ploufragan-Plouzané
Unité Génétique Virale et Biosécurité
22440 Ploufragan
Tel : (33) 02 96 01 62 71
6 years
Fatal Error while uploading a File with special Characters
by Matthias Enders
Dear Galaxy Community,
a User of our Galaxy Platform has produced a fatal error by uploading a file containing a German special character (ä / ü / ö / ß). This resulted in the following status (only for the given user):
- Upload was canceled: Status was "Failed Internal Server Error (500)"
- All Histories were corrupt stating: "An error was encountered while loading the contents."
- Tools can´t be used an stating (in Traceback):
" UnicodeDecodeError: 'utf8' codec can't decode byte 0xfc in position 5: invalid start byte"
"Module weberror.evalexception.middleware:364 in respond"
This totally destroyed to current user and we have had to purge him in order to get him back to work, even losing all his datasets & histories!
We are using an MySQL database as a backend. Is the Encoding of this database the problem? If yes: Which encoding is used/supported by galaxy?
Thanks in advance!
Matthias
6 years
Configuring Apache server with uwsgi
by Makis Ladoukakis
Hi everyone,
I am setting up a galaxy instance in my university server that has 64 cores (4 cpus 16 threads each) and 512GB of memory and I am trying to figure out the best configuration in order to exploit it as best as we can. We are planning to use it for about 100-200 people.
So far I followed the instructions in
https://wiki.galaxyproject.org/Admin/GetGalaxy
https://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
and
https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
but I found a little bit confusing the different instructions for Paste based processes and uwsgi. I'm planning to use uwsgi in Apache.
So I've been using mysql as the galaxy database
and added the following part in galaxy.ini
[uwsgi]
processes = 12
stats = 127.0.0.1:9191
socket = 127.0.0.1:4001
pythonpath = lib
threads = 4
logto = /home/galaxy/uwsgi.log
master = True
[server:handler0]
use = egg:Paste#http
port = 8090
use_threadpool = True
threadpool_workers = 10
[server:handler1]
use = egg:Paste#http
port = 8091
use_threadpool = True
threadpool_workers = 10
[server:handler2]
use = egg:Paste#http
port = 8092
use_threadpool = True
threadpool_workers = 10
[server:handler3]
use = egg:Paste#http
port = 8093
use_threadpool = True
threadpool_workers = 10
[server:handler4]
use = egg:Paste#http
port = 8094
use_threadpool = True
threadpool_workers = 10
[server:handler5]
use = egg:Paste#http
port = 8095
use_threadpool = True
threadpool_workers = 10
# The port on which to listen.
#port = 8090
>From a previous post i got that you are using 6 handlers for usegalaxy.org so I figured I'd start with that.
Could you help me configure my apache server? So far I've added the following in the apache configuration file:
RewriteEngine on
RewriteRule ^(.*) http://localhost:8090$1 [P]
RewriteRule ^/galaxy$ /galaxy/ [R]
RewriteRule ^/galaxy/static/style/(.*) /home/nate/galaxy-dist/static/june_2007_style/blue/$1 [L]
RewriteRule ^/galaxy/static/scripts/(.*) /home/nate/galaxy-dist/static/scripts/packed/$1 [L]
RewriteRule ^/galaxy/static/(.*) /home/nate/galaxy-dist/static/$1 [L]
RewriteRule ^/galaxy/favicon.ico /home/nate/galaxy-dist/static/favicon.ico [L]
RewriteRule ^/galaxy/robots.txt /home/nate/galaxy-dist/static/robots.txt [L]
<Location "/galaxy">
Sethandler uwsgi-handler
uWSGISocket 127.0.0.1:4001
uWSGImaxVars 512
</Location>
But I'm not sure how Apache will proxy the different ports from the handler. In the Apache configuration instructions it said I should use a balancer but in the Scaling instructions it states that this is for standalone paste-based processes.
Could you help me out please?
Thank you,
Makis
6 years
galaxy.ini tool_dependency_dir change
by Dooley, Damion
On a VM I moved the tool_dependency_dir folder to another mount since it was getting so large that the smallish main mount was full (and changed galaxy.ini, restarted galaxy, and checked that permissions were appropriate for galaxy user). But I'm finding I have to reinstall various tool dependencies (prokka etc) to enable galaxy to find the command line executables. Is there a trick to getting the tool dependencies working again after moving the folder wholesale?
Thanks,
Damion
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
6 years
BUG: Collections and History export
by Alexander Vowinkel
Hi,
when downloading/exporting a history via the interface,
visible collections are not being exported.
The contents of the collection(s) are hidden,
the Colleciton itself is visible.
Best,
Alexander
6 years
Connection to PBS server XXX for state check failed
by Zuzanna K. Filutowska
Dear All,
I encountered exactly the same problem:
http://osdir.lowified.com/galaxy-development-source-control/2012-07/msg00...
However my Galaxy instance completely crashes until restart, I am
getting Proxy Error on HTTPd. Any help would be much appreciated, as we
will have Galaxy workshop on Monday at our University.
In logs I have:
galaxy.jobs.runners.pbs DEBUG 2015-09-09 15:04:21,306 connection to PBS
server ce.reef.man.poznan.pl for state check failed
galaxy.jobs.runners.pbs DEBUG 2015-09-09 15:04:21,380
(441/13320109.ce.reef.man.poznan.pl) Skipping state check because PBS
server connection failed
galaxy.jobs.runners.pbs DEBUG 2015-09-09 15:04:21,430
(444/13320114.ce.reef.man.poznan.pl) Skipping state check because PBS
server connection failed
+2+12+19+6galaxy+0+32+12+9job_state+1+0+0+02+172+14resources_used+1+0+0
+02+142+11exit_status+1+0+0+0+0
But the PBS server works fine.
--
Pozdrawiam,
--
Zuzanna K. Filutowska, HPC Systems Administrator
Poznan Supercomputing and Networking Center
Institute of Bioorganic Chemistry Polish Academy of Sciences
Seize the day boys! Make your lifes extraordinary! --John Keating
6 years
