instances both pointing to the
same FTP upload directory. The idea seems sound in my head but I want to
make sure I'm not excluding any critical considerations. Any suggestions or
insights would be appreciated.
Thanks,
Josh Nielsen
HudsonAlpha Institute for Biotechnology
the suggestion here:
http://stackoverflow.com/questions/10220531/how-to-set-system-wide-umask).
Still no dice. I've pretty much exhausted my know-how in this department.
Any other suggestions of how to fix this or where the correct place to set
the umask is?
Thanks,
Josh Nielsen
)
$0 stop; $0 start
;;
*)
echo Usage: galaxy
{start|stop|status|reload|restart}
;;
esac
--
Thanks!
Josh
On Tue, Dec 4, 2012 at 9:56 AM, Nate Coraor n...@bx.psu.edu wrote:
On Dec 4, 2012, at 10:52 AM, Josh Nielsen wrote:
Hello all
, Dec 4, 2012 at 10:06 AM, Paul Boddie paul.bod...@biotek.uio.nowrote:
On 04/12/12 16:52, Josh Nielsen wrote:
I am getting the error (13)Permission denied: xsendfile: cannot open
file:
/basedir/galaxy_data/database/**tmp/tmp8iEccn/library_**download.zip
which is
indeed a basic filesystem
AM, Josh Nielsen wrote:
Hi Nate,
Thanks for the reply. No I hadn't thought to add anything to
/etc/init.d/galaxy itself. It is a short enough script that I can paste it
below. What would I need to do to edit it with umask settings?
Also I should note, changing the umask in the PAM
that
doesn't fix it.
-Josh
On Mon, Oct 1, 2012 at 11:33 AM, Nate Coraor n...@bx.psu.edu wrote:
Hi Josh,
Are you using XSendFile or X-Accel-Redirect, by any chance?
--nate
On Sep 17, 2012, at 5:18 PM, Josh Nielsen wrote:
Okay, I solved half of the problem. The upload job was consistently
the data to a new
location and change the path variables in universe_wsgi.ini. Any
suggestions on the proper changes that need to be made to fix this
permanently?
Thanks,
Josh Nielsen
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to do away with the symlink approach altogether and get Galaxy to work
directly with the new directory path. Any suggestions for getting that to
work?
Thanks!
On Mon, Sep 17, 2012 at 3:50 PM, Josh Nielsen jniel...@hudsonalpha.comwrote:
Hello all,
I recently migrated the location of the Galaxy
have a Centos machine
here at the moment, but I think if you install OpenJDK and use the
alternatives system to select that as the default JRE then that should fix
things.
Simon.
On 25 Jun 2012, at 17:19, Josh Nielsen wrote:
Hi Simon,
I recently installed Java with the yum package manager
?
Thanks!
On Fri, Jun 22, 2012 at 5:35 PM, Ross ross.laza...@gmail.com wrote:
Do you run an X11 virtual frame buffer - eg Xvfb?
Otherwise AFAIK R graphics and Java will complain on headless nodes.
On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen jniel...@hudsonalpha.com
wrote:
Hello,
I am
JRE (or update your
path to point to one which is already present).
Simon.
On Sat, Jun 23, 2012 at 6:30 AM, Josh Nielsen jniel...@hudsonalpha.com
wrote:
Hello,
I am having an issue with getting the FastQC tool to work with Galaxy on
our
server. I downloaded the FastQC files (version
system to select that as the default JRE then that should fix
things.
Simon.
On 25 Jun 2012, at 17:19, Josh Nielsen wrote:
Hi Simon,
I recently installed Java with the yum package manager on our compute
nodes, and our cluster is a Centos 6 environment. Here is what the results
of java
Hello,
I am having an issue with getting the FastQC tool to work with Galaxy on
our server. I downloaded the FastQC files (version 0.8.0) and changed the
directory that the wrapper script looks for the 'fastqc' executable in, but
when we run a job with it we have been getting the following
Ah, yes. This is what I was just requesting yesterday in the email
that I sent, although it was much more long-winded. I didn't see this
email chain from the day before. Having a user-representative
directory structure would be beneficial in my mind.
I followed/understood your suggested directory
I have seen this error many times (for various mako.py files) and it is
often either when the user running it has insufficient privileges or the
file permissions on a folder (could be several directories upstream) or a
file have changed in some way. If you do a 'ps -ef | grep python' do you
see
caught that so I guess I just
didn't understand what you were getting at.
Josh Nielsen
--
How about if there were a completely separate daemon that monitored the galaxy
database periodically to determine what datasets belong to which user(s). Then
it would move the actual dataset
, and that
the permissions be kept correct. Typically users have no idea what is
going on with their permissions, so what are you going to do?
David
On May 16, 2012, at 1:33 PM, Josh Nielsen wrote:
Hi David,
Actually that is an interesting idea to use a daemon to move the files
into associated user
. But a file-system hierarchy alternative would also be welcome in a
heavily command-line oriented computational environment too.
Would setting up a more user-representative output directory hierarchy on
the file-system like that be possible?
Best Regards,
Josh Nielsen
to try to figure out what went wrong with the current
install. However I'm not having any breakthroughs and our local Galaxy
mirror has been down for over a week now and I just want to start fresh and
migrate over critical data if possible.
Thanks for your help,
Josh Nielsen
. A lot of our users are heavy
into informatics though and would probably prefer that the user be able to
see that information. Does anyone have any suggestions or thoughts about
this?
Thanks,
Josh Nielsen
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make a new option in the universe.ini file for that purpose
that can be set for people who want it?
Thanks,
Josh Nielsen
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are:
# always, onsuccess, never
#cleanup_job = always
On Apr 24, 2012, at 5:00 PM, Josh Nielsen wrote:
Hello again,
As I mentioned in a recent post I often find need to debug jobs running
from our local Galaxy mirror and I often have the need to look at the
script data files that the job is trying
Hello all,
I am having some trouble getting a display at link to my local UCSC
Genome Browser mirror to show up under my Galaxy jobs for viewing, although
I can get the link to the online UCSC GB to display. I followed the
suggestions in the following thread but it has yielded no results yet:
. Can you check that the line you copied is tab
delimited and not space delimited?
Thanks for using Galaxy,
Dan
On Feb 27, 2012, at 11:46 AM, Josh Nielsen wrote:
Hello all,
I am having some trouble getting a display at link to my local UCSC
Genome Browser mirror to show up under my
internalgb entry to the new tool_id I created is there?
On Mon, Feb 27, 2012 at 11:58 AM, Josh Nielsen jniel...@hudsonalpha.comwrote:
Hi Dan,
Good catch sir! Genius! It is working now. The spacing was exactly the
same to the eye in vi for all the entries, but once I did a 'set list' in
vi
at 11:08 AM, Josh Nielsen jniel...@hudsonalpha.comwrote:
Also, I just uploaded a 1.3GB FASTQ file and the small preview box in the
history pane shows the first few lines, and when I click on the eye it
actually displays in the window with the message This dataset is large and
only the first
Ah, following the lead in the log paid off. I had to add the statement
*XSendFilePath
/panfs/galaxy_data *to /etc/httpd/conf/httpd.conf. Apparently ever since I
had moved the dataset directory to /panfs/galaxy_data by setting the
file_path variable in universe_wsgi.ini I have not attempted to view
Hello all,
I recently have been having problems viewing/displaying datasets (with the
eye icon) as well as downloading datasets in Galaxy which I have uploaded,
although I can actually point to those datasets as input to other tools and
they show up on the drop down menus and it runs perfectly.
.
-Josh
-- Forwarded message --
From: Josh Nielsen jniel...@hudsonalpha.com
Date: Tue, Jan 17, 2012 at 10:22 AM
Subject: Issues displaying/downloading datasets
To: galaxy-dev@lists.bx.psu.edu
Hello all,
I recently have been having problems viewing/displaying datasets (with the
eye icon
Thanks Nate! Updated documentation is always welcome and useful. I
appreciate the clarifications.
-J
On Mon, Dec 12, 2011 at 10:18 AM, Nate Coraor n...@bx.psu.edu wrote:
On Dec 9, 2011, at 4:34 PM, Josh Nielsen wrote:
Hello,
I have a question which I have not seen specifically addressed
if it only showed an example for one or two
specific tools.
I looked a bit but couldn't find it; I suspect it is out on the wiki
somewhere, though clearly it needs to be easier to find.
Good luck,
J.
--
Josh Nielsen
Systems Administrator
HudsonAlpha Institute for Biotechnology
256-319
on this
please? Adding a brief page on the Galaxy wiki site under the Admin section
about this would really help, even if it only showed an example for one or
two specific tools.
Thanks,
Josh Nielsen
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