Thanks for the tip Eric. I was able to figure it out. The key to this,
was you suggested was permission issue.
I had to modify sudoers so tty was not required. This will allow
scripts to change ownership to the correct user so SGE can submit
them.
Thanks!
-Adam
--
Adam Brenner
Computer Science
Anyone have any ideas on this?
Thanks,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
System Administrator, HPC Cluster
Office of Information Technology
http://hpc.oit.uci.edu/
University of California, Irvine
system_pwent[0], str(
self.galaxy_system_pwent[3] ) )
File "/data/apps/galaxy/dist/lib/galaxy/jobs/__init__.py", line
1302, in _change_ownership
assert p.returncode == 0
AssertionError
Any idea on how to fix the issue?
Thanks,
-Adam
--
Adam Brenner
Computer Science, Undergraduate
ng DRMAA APIs would be
great. If this tool can parallel fastq jobs along with BAM as described, it
would be a great improvement for a number of people here.
~Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computin
been setup to handle static content?
To many unknowns
~Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California
eally from our users.
Do you know which of the python files contain the code that relates to
this? Or point me in the right direction so I can change this?
Thanks!
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Comp
address is that of the user?
Thanks,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California, Irvine
www.ics.uci.edu/~aebrenne
importing a few tables (such as users) into the new galaxy DB..but I am not
sure. Perhaps someone more familiar with the Galaxy DB can comment on this.
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of
roughly ~one month old: c42567f43aa7.
[1]:
http://dev.list.galaxyproject.org/Looking-for-recommendations-How-to-run-galaxy-workflows-in-batch-td4362836.html#a4362874
Thanks!
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Carlos,
Are you using any sort of scheduler? SGE/Torque, etc? How are jobs being
dispatched to your node(s)? More info here:
http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer
like the idea, folks like me who
really do care about the version of GCC we use (and compile our
own versions of gcc) will not use it. However, that is going off topic
now :-)
Will wait and see what others say...
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Infor
their own if it was
on a separate mailing list It would be easier to search and look
back at previous threads.
However, the added benefit of having the devel list is that we get
feedback from Galaxy Developers
As the saying godes: Just food for thought,
-Adam
--
Adam Brenner
Computer Science
galaxy-dist/
$ cd galaxy-dist
$ hg update stable
If you are running into issues, can you be more specific...provide
error message? Steps on how to reproduce your issue?
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing
://wiki.galaxyproject.org/Admin/Get%20Galaxy
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre
://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California, Irvine
www.ics.uci.edu
n your own read/write tests.
When I was using ZFS, this ZFSBuild[2] website was most helpful.
Let me know if you have any other questions,
-Adam
[1]: http://www.gluster.org/pipermail/gluster-users/2012-September/034295.html
[2]: http://www.zfsbuild.com/
--
Adam Brenner
Computer Science, Undergr
Jim,
You need to enable Apache's proxy service. See my pervious post here:
http://dev.list.galaxyproject.org/Running-Galaxy-through-Apache-td4659452.html
Let us know if you run into further issues,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Inform
nup_datasets
> directory and are named:
Should be changed to 6 scripts
Thanks,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
Unive
Alper,
Nginx or Apache? Did you modify universe_wsgi.ini and add the proxy
settings?
Does the information on
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Using_a_proxy_serverhelp
you?
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of
Hamid,
Read the information here:
http://snpeff.sourceforge.net/SnpEff_manual.html#galaxy
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs
tication-td4659271.html
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu
On
The issue here is the last line:
OperationalError: (OperationalError) disk I/O error u'PRAGMA
table_info("dataset")' ()
Do you have any security rules setup on the server, quotes, disk
issues, etc? You can always run a strace on run.sh for a better
understanding of what
l
should be ran, cluster, local, etc.
[1] http://wiki.galaxyproject.org/Admin/Config/Jobs
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
U
May you make your question more specific? Have you read the online
docs: http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information
When you updated, did you download all the files? Was their any
conflicts during the update? It appears you are missing a file.
Cant locate template for uri 'root/index.mako'
Run 'hg update'...
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren Schoo
-request/192/express-tool-requirements-tag-updated/diff
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California, Irvine
ncy/eXpress/
|---default --> 1.3.0
|1.3.0/env.sh
Thanks,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California,
Bart,
I believe drmaa://-q somehost@queue-name
will work. However I could be very wrong. It has been a while since I
messed with the actual drmaa runners.
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
?
Thanks in advanced!
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre
Why not use Allow All / Deny All rules?
... your Auth Type stuff here ...
Deny from all
Allow from 127.0.0.1 # Assuming API calls are made locally
Satisfy any
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research
, can it be configured to
> do so?
You will need to configure your job runners and job workers for this.
http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
Enjoy!
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Scienc
How are you trying to upload the data to Galaxy? Are you using the web
interface? Or...?
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs
cluster storage
pool of 600TB.
We use the gluster filesystem across 6 storage nodes. We are trying
fhgfs and other file systems as well (lustre, ceph, etc).
If you have any other questions, feel free to ask.
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of
Greg,
Thanks for the tip on Safari. I have switched to another browser and
working now!
Thanks,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http
and could not find anything
that looks like Galaxy URL. Any ideas on how to set the Galaxy URL?
Thanks,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http
l'
then manually move the binary files it produces into some
environmental $PATH.
Hope that helps,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.o
Proxy page as its missing information..feedback is appreciated).
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California, I
Jeff,
Did you ever get this to work?
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California, Irvine
www.ics.uci.edu
What version of Python are you using? I believe Python 2.7 is the recommend
version. I suggest you grab a fresh copy of galaxy from the stable branch
and try again.
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing
hair pulling and waiting response from IRC to figure this
out...wasn't fun.
As for your issue, you want to specify your handlers, not your
webserver for your handler types.
Let me know if this helps,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren Scho
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California, Irvine
www.ics.uci.edu/~aebrenne/
aebre...@uci.edu
On Tue, Apr 30, 2013
/galaxy http://localhost:8080/
# Line below is optional
Redirect permanent /galaxy http://mymachine.com/galaxy
ProxyVia On
Let us know,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office
Galaxy... and thus offering us
less fine grain control to Galaxy.
Anything anyone has to share would be much appreciated,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information
, Adam Brenner wrote:
> Anyone have any ideas as to why its not running? Surely must be a few
> users who run Galaxy via a Scheduler using DRMAA...
>
> My updated job_conf.xml is like so: http://pastebin.com/raw.php?i=QJbay57i
>
>
> Jobs do get submitted to DRMAA, but the scr
set to true in universe_wsgi.ini and nothing
regarding errors or debug message are created in paster.log about this.
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http
thing
will be displayed in Galaxy. It does support nested folders, etc...
Hopefully that helps,
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.ed
Um... Lets see Jillian. Can the user who is running the Galaxy process
access the folders in question? Whats the chown/chmod on the folders?
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of
restart.
We have the same setup on our HPC cluster. Users copy their data to
the large storage bricks via scp, rsync, etc...
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
John, that worked! I was able to upload some sample files using usernames,
rather then full email address. No errors, no bugs.
Thanks!
-Adam
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of
/tmp/user); do ln -s /gl/tmp/user /gl/tmp/u...@uci.edu
;done;
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California, Irvine
#Submitting_Jobs_as_the_Real_User
Any ideas as to why galaxy_external* is not being called? The paster.log
file does not show anything useful regarding calling external scripts.
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
So I finally figured it out (thanks to the help from the IRC folks, bag and
natefoo).
I incorrectly had my job_conf.xml setup where no job runners were set. All
is working now.
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Anyone have any ideas? Still have not sorted this out
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of California, Irvine
pr/2013:13:24:44 -0700] "GET
/api/histories/56959efe847bb360 HTTP/1.0" 200 - "
http://ghtf-hpc.oit.uci.edu/history"; "Mozilla/5.0 (Macintosh; Intel Mac OS
X 10_8_3) AppleWebKit/536.28.10 (KHTML, like Gecko) Version/6.0.3
Safari/536.28.10"
--
Adam Brenner
Computer Scie
sions on the my file_path or new_file_path directories?
A very stumped Adam.
--
Adam Brenner
Computer Science, Undergraduate Student
Donald Bren School of Information and Computer Sciences
Research Computing Support
Office of Information Technology
http://www.oit.uci.edu/rcs/
University of Cal
55 matches
Mail list logo
