Dave Walton wrote:
Could someone who has successfully gotten the IGV tool to work using NGINX as
your proxy, tell me if there was anything specific they needed to do with
their NGINX or galaxy config to get it working?
Hi Dave,
It's necessary to set up the more advanced configuration under
Liisa Koski wrote:
Is it possible to run a specific workflow only on certain nodes of the
cluster? Either using the API or by setting something in the config files?
Hi Liisa,
Galaxy currently only allows specification of these sorts of parameters
on a per-tool basis, so it's not possible to
Matthew Conte wrote:
Good afternoon,
I'm having several problems with my local galaxy install which may or may
not be related to one another.
The first problem I'm having is with the Display data in browser feature.
Some files type formats (fastqsanger, fasta) display fine. However,
Matthew Conte wrote:
Hi Nate,
Yep, I'm using mod_xsendfile-0.12 for apache and x-accel-redirect for nginx,
but both webservers are showing the same problems. If I use Galaxy's
built-in webserver, I don't have the above problems, so the problem is
probably related to the proxy server. I
configurations, off-list please.
Thanks,
--nate
Thanks,
Matt
On Mon, May 9, 2011 at 4:15 PM, Nate Coraor n...@bx.psu.edu wrote:
Matthew Conte wrote:
Hi Nate,
Yep, I'm using mod_xsendfile-0.12 for apache and x-accel-redirect for
nginx,
but both webservers are showing the same
Vipin TS wrote:
Dear Galaxy Team,
I am switching our Galaxy production service to a new machine, We are using
Postgres as database server.
The existing database belongs to postgres version 8.3 and I took my
instance's dump using postgres version 8.4.
I am able to restore my database on
Marco Moretto wrote:
Hi all,
I successfully installed a Galaxy instance locally. I use Galaxy with
Apache. Every time I try to download a file from history (like Options -
Export to file) the browser (Firefox 3.6) reply with the error
/tmp/lFeL6erm.asc.part could not be saved, because the
Liisa Koski wrote:
Hi,
Yesterday I ran the cleanup_datasets.py scripts as follows..
Deleting Userless Histories
python cleanup_datasets.py universe_wsgi.ini -d 10 -1
Purging Deleted Histories
python cleanup_datasets.py universe_wsgi.ini -d 10 -2 -r
Purging Deleted Datasets
python
Duddy, John wrote:
I'm looking at extending the metadata fields for one of the supported file
types. The files can get VERY large, and since I'm creating those files, I'd
like to save as metadata some of the information I have on the contents.
Specifically, I'd like to tag the files with
Marina Gourtovaia wrote:
Line 298 of galaxy-dist/tool_conf.xml in the zipped distribution
downloaded yesterday
tool file=indels/indel_table.xml /
should be
tool file=indels/indel_table.xml /
?
Hi Marina,
Indeed, thanks for catching this. It has been fixed and will go out in
the
Yamshchikov, Vladimir wrote:
Hello all,
If this question is not for this list, please advise. Both my RHEL55 and SL55
are based on python 2.4.3 - how I can add python 2.6 support for Galaxy
without screwing up OS? I had both 2.4 and 2.6 installed, by python -V
returns only 2.4.3. When
/galaxy/galaxy-dist
4. Given the above details, can I just execute 4?
Yes, you should be able to. That version of postgres is rather old but
psycopg2 should be backwards compatible.
--nate
Thank you
Nikolay
On Mon, 2 May 2011 10:27:41 -0400, Nate Coraor n...@bx.psu.edu wrote:
Nikolai
Nikolai Vazov wrote:
Hi again,
The version of the PostgreSQL server I am trying to connect to is
actually 8.3. The DB department say they will soon move to 9.0.
The psycopg2 version in my eggs.ini for Galaxy is 8.4.2:
psycopg2-2.0.13_8.4.2_static-py2.6-linux-x86_64-ucs4.egg
Do you
Nikolai Vazov wrote:
Hi, Nate,
When trying to execute
PYTHONPATH=/home/galaxy/galaxy-dist/scripts/scramble/lib python26
setup.py egg_info --tag-build=_8.4.2_static bdist_egg
I get
Traceback (most recent call last):
File setup.py, line 52, in module
from scramble_lib import
Nikolai Vazov wrote:
Hi,
I am trying to connect my galaxy instance to a DB on a different
host. This DB uses an SSL encryption and Auth method md5.
I have no problems in connecting to the DB via the command line, but
the line (in universe_wsqi.ini) :
database_connection =
Nikolai Vazov wrote:
Hi, Nate,
Thanks a lot for the hint : I also had suspicions about the SSL and
it seems to be working, well, I mean, failing, as you supposed
because of my psycopg2 which was built without SSL.
OperationalError: (OperationalError) sslmode value require invalid
George Yianni Michopoulos wrote:
To any wonderful person that can help me:
I recently uploaded a local instance of Galaxy on a new computer at the
Fernald Lab at Stanford. I am not too familiar with Unix, but needed to
install the local instance due to the high volume of genomic data
Assaf Gordon wrote:
I'll rephrase my question:
Is cython going to be a standard requirement for Galaxy (and needs to be
manually installed on our production servers), or is this just a temporary
thing, or is it going to be an automatic egg thing ?
No, that's a mistake. I should have a fix
Pieter Neerincx wrote:
Hi Leandro,
On Apr 27, 2011, at 6:08 PM, Leandro Hermida wrote:
Hi Pieter,
cut
I have this *exact* same setup as you where I am authenticating with the
LDAP user ID and returning a mail LDAP attribute as REMOTE_USER, but this
sets the Galaxy user email
Leandro Hermida wrote:
Hi everyone,
Has anyone actually properly implemented remote_user_logout_href in Galaxy
with external HTTP authentication? As probably those who have tried know,
it is rife there doesn't seem to be a clean and robust way to do this?
Hi Leandro,
Other than loading in
Leandro Hermida wrote:
Sorry one more question... are these lines in the Galaxy wiki instructions
still correct for the latest galaxy-dist?
They should be, yes.
RewriteRule ^/galaxy/static/style/(.*)
/home/nate/galaxy_dist/static/june_2007_style/blue/$1 [L]
RewriteRule
Assaf Gordon wrote:
Forgot to mention SGE/PBS: you definitely want to use them (even if you're
using a single machine),
because the local job runner doesn't take into account multi-threaded
programs when scheduling jobs.
So another core is needed for the SGE scheduler daemons (sge_qmaster
andrew stewart wrote:
I'm aware of how to configure Galaxy to use SGE in universe_wsgi.ini,
however what I want to do is a little different. Because I only want
certain processes to be submitted to the queue, I'd rather control this at
the tool configuration level (the xml wrapper). For
Ryan Golhar wrote:
Nate - Is there a way to get the pbs job scripts to still get saved
with debugging turned off? I'm running into this same problem but
still prefer to have the job scripts kept in case something goes
wrong.
Not without modifying the call to cleanup() in the job runner
CHAN Chee Seng wrote:
Hi Ryan,
Thanks for sharing the work around.
I had the same problem. I am running galaxy with mysql server. I tested on
1. Firefox on a linux box
2. IE and firefox on a windows box.
I tried restarting galaxy and the apache httpd server and my client machines
Musa A. Hassan wrote:
I am trying to use galaxy for the first time and am running into some early
problems. While trying to upload my file which is basically an fq containing
illumina short reads, the file won't upload. When I try the fastq extension
of the same file, it does but then the
-in limitations on file size/count.
--nate
Please find the attached screenshoots for your reference.
Looking forward to hearing from you.
Best Wishes,
Yan
On Tue, Feb 15, 2011 at 9:08 AM, Nate Coraor n...@bx.psu.edu wrote:
Yan Luo wrote:
Dear Nate,
Yes, you are right
Ryan Golhar wrote:
I have a local instance running. When I'm logged in as user1, log
out, then try to log in as user2, I keep getting the You have been
logged out message.
Its as if the browser's cache is retaining some information. To get
around this, after I log out as user1, I have to
Peter Cock wrote:
On Mon, Mar 7, 2011 at 5:56 PM, Nate Coraor n...@bx.psu.edu wrote:
Ryan Golhar wrote:
I have a local instance running. When I'm logged in as user1, log
out, then try to log in as user2, I keep getting the You have been
logged out message.
Its as if the browser's
Sarah Diehl wrote:
Hi all,
I'm currently working on setting up a fresh Galaxy server at our
institute. I'm going through the tool dependencies list and install
everything on it. I installed the latest R version (2.12.2) and now
I'm trying to install rpy. With some workarounds I managed to
,
Sonali
-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: Tuesday, February 15, 2011 10:30 PM
To: Sonali Amonkar
Cc: Galaxy Dev
Subject: Re: [galaxy-dev] Error with setuptools version in Galaxy
installation on Cluster
Sonali Amonkar wrote
Jean-Baptiste Denis wrote:
Hello everybody,
i've got one galaxy server running. The ressource on the wiki are very
useful for that purpose, thank you.
I've got one question regarding data library when using upload files
from filesystem paths. There is a checkbox, unchecked by default,
Conference as they will be able to interact with key Galaxy Team
members such as Nate Coraor, who runs Penn State instance here.
Thanks!
anton
On Feb 25, 2011, at 6:14 AM, Lee Hazelwood wrote:
Dear Prof Nekrutenko,
The university where I work is looking to locally implement
hari krishna wrote:
Hi ,
Can any one help me how to transfer files from head node to remote
location by using DRMAA job template attributes with example will DRMAA
supports staging in and staging out of files,...
Hi,
You can use the drmaa_transfer_files job template attribute,
Peter Cock wrote:
File
/home/galaxy/galaxy-dist/lib/galaxy/web/framework/helpers/__init__.py,
line 29
return (content if len(content) = length else content[:length].rsplit('
', 1)[0]+suffix)
^
SyntaxError: invalid syntax
I deduce you're using Python 2.4,
Glen Beane wrote:
We run a local galaxy instance with multiple galaxy web servers and a job
runner. Per the wiki suggestion we have two config files:
universe_wsgi.webapp.ini and universe_wsgi.runner.ini. I've noticed that we
still need universe_wsgi.ini or else galaxy will not start
Hi
Ry4an Brase wrote:
I'm working on getting more of our jobs offloaded to other machines, and
I'm getting job failures I'm not able to debug. When running a simple
tool like 'cut', submitted over qsub, I'm getting STDERR output like
this:
WARNING:galaxy.datatypes.registry:Error loading
Ryan Golhar wrote:
I've configured my local instance of galaxy to run with drmaa.
Unfortunately, there is a problem that after some time, galaxy loses
its ability to talk to Torque, hence Galaxy thinks long-running jobs
have failed and its unable to submit new jobs.
I have no idea how this
Steve Taylor wrote:
I think so. Just to double check is there a definitive way I can tell? In
./tools/data_source/upload.xml
param name=ftp_files type=ftpfile label=Files uploaded via FTP/
So I got this to work by hacking basic.py.
def visible( self ):
/11 05:58, Nate Coraor wrote:
Hi Florent, et. al.,
I've moved the discussion over to galaxy-dev since it pertains to local
instances.
Florent Angly wrote:
Indeed, this workaround works! Thank you.
I added these lines to the beginning of my run.sh:
PATH=/opt/local/bin:/opt/local/sbin
Marina Gourtovaia wrote:
Hi
In a bash shell, I define the path (needed both by Galaxy to find
the right version of python and by tools that run on a cluster to
find the executables) and some other global variables on the
command line. The cluster jobs (LSF) inherit all these values. This
Peter wrote:
On Mon, Feb 21, 2011 at 2:43 PM, Nate Coraor n...@bx.psu.edu wrote:
Revival! (This thread was sitting flagged in my mailbox since
November)
I guess I should try and file issues for things which don't get a prompt
resolution on the mailing list, but its good to know it hadn't
Nick Schurch wrote:
Hi all,
I've recently encountered a few problems when trying to use Galaxy which are
really driving me away from using it as a bioinformatics platform for NGS. I
was wonderinf if there are any simple solutions that I've missed...
Hi Nick,
We've had some internal
Ryan Golhar wrote:
I've implemented the Serving Galaxy at a sub directory (such as
/galaxy), made the change to Apache, and the universe_wsgi.ini.
When I view the page through Apache using http://server.name/galaxy,
the page is garbled like something didn't take.
Hi Ryan,
Did you
Ryan Golhar wrote:
SOLVED. I copied/paste the Rewrite rules for apache from the wiki
without updating the paths to my installation...once I did that, all
worked well.
Whoops, I should read ahead before I reply. Glad it's working!
--nate
On 2/17/11 5:07 PM, Ryan Golhar wrote:
I've
Ryan Golhar wrote:
Nevermind (once again). I figured out I need to compile it from the
torque...
You can also use the 'pbs' job runner, which wraps the PBS C API
directly instead of using DRMAA.
--nate
On 2/17/11 10:30 PM, Ryan Golhar wrote:
I'm configuring my local install of galaxy to
Ryan Golhar wrote:
It turns out the user's environment is not set up for batch jobs,
only the system environment. I too added . ~/.bashrc to
lib/galaxy/jobs/runners/drmaa.py.
I'm afraid this is a kludgy fix that will break if/when the drmaa.py
file gets updated. It'll work for now, but
Pauras P Patil wrote:
Hello,
I am currently working on a project related to bioinformatics here at Purdue
University and we wanted a tool that could create a workflow for the data
that we collect. I have downloaded the source code for galaxy, but have no
idea on how to integrate galaxy
David Hoover wrote:
This used to work. Now when I try to upload a directory of files, it gives
this error:
URL:
https://galaxy.cit.nih.gov/library_common/ldda_info?library_id=a799d38679e985dbshow_deleted=Falsecntrller=libraryfolder_id=0a248a1f62a0cc04use_panels=Falseid=dff4190d282fb07a
Ryan Golhar wrote:
I've set up a local instance of Galaxy following the instructions in
the wiki for a production instance. I'm running on CentOS with
Apache, and a mysql database server.
Everything looks great when viewed directly through the Galaxy web
server on port 8080.
I've
pull -u http://bitbucket.org/galaxy/galaxy-central/
--nate
Looking forward to hearing from you.
Thanks,
Yan
On Thu, Feb 10, 2011 at 10:26 PM, Nate Coraor n...@bx.psu.edu wrote:
Yan Luo wrote:
Dear Nate,
Please find the following errors, it is the newest, and our restart
Wishes,
Yan
On Fri, Feb 11, 2011 at 8:45 AM, Nate Coraor n...@bx.psu.edu wrote:
Yan Luo wrote:
Dear Nate,
Why did you say we have 3 paths? We have a link from
/home/kangtu/Downloads/galaxy-dist
lrwxrwxrwx 1 kangtu admin36 2010-11-01 17:07 galaxy-dist -
/home
Glen Beane wrote:
On Feb 9, 2011, at 9:44 AM, Glen Beane wrote:
I've been doing some testing with a Galaxy instance running on my laptop
for some tools we are developing. I am uploading a file into Galaxy from a
URL to use as test input (~1.5GB tabular) I can download this file to my
Yan Luo wrote:
Dear Nate,
I just run the first step and must use sudo to wget and it is ok.
Otherwsie, I can't write (Cannot write to `virtualenv.py.1' (Success).)
I would strongly advise against using sudo for any part of this, since
this is how permissions get screwed up. If you don't
pip-2.6
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$
Could you please let me know if you have any suggestion?
Best WIshes,
Yan
On Fri, Feb 11, 2011 at 10:05 AM, Nate Coraor n...@bx.psu.edu wrote:
Yan Luo wrote:
Dear Nate,
I just run the first step
.
Best Wishes,
Yan
On Fri, Feb 11, 2011 at 10:31 AM, Nate Coraor n...@bx.psu.edu wrote:
Yan Luo wrote:
Dear Nate,
When I run .
/home/kangtu/data/tools/galaxy-dist/galaxy_env/bin/activate
directly,
kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ .
/home
Glen Beane wrote:
On Feb 11, 2011, at 9:32 AM, Nate Coraor wrote:
Glen Beane wrote:
On Feb 9, 2011, at 9:44 AM, Glen Beane wrote:
I've been doing some testing with a Galaxy instance running on my laptop
for some tools we are developing. I am uploading a file into Galaxy from
Sonali Amonkar wrote:
I am currently facing another issue. When I run my Workflow, I am seeing the
following error on the server log. This error is not consistent, and occurs
in an erratic manner.
galaxy.jobs INFO 2011-02-03 05:17:03,522 job 151 dispatched
galaxy.jobs.runners.pbs
Nate Coraor wrote:
Sonali Amonkar wrote:
I am currently facing another issue. When I run my Workflow, I am seeing
the following error on the server log. This error is not consistent, and
occurs in an erratic manner.
galaxy.jobs INFO 2011-02-03 05:17:03,522 job 151 dispatched
Vipin TS wrote:
Hi all,
Last day we upgraded our galaxy service computing cluster nodes operating
system from Ubuntu hadry to lucid 10.4. We updated python eggs and now
getting an Warning message, it apparently kills the galaxy jobs. Warning
message as follows:
Yan Luo wrote:
Dear Nate,
Please find the following errors, it is the newest, and our restart is
stopped. I hope we can get the solution from you as soon as possible.
Hi Yan,
Your last 4 messages included 3 different paths to Galaxy. It seems as
though there are quite a few copies of
My thanks as well, since we don't really have a way to debug LSF here.
Platform only granted us a 1 month license for the development, so I'd
have to get another license to debug it.
--nate
Leandro Hermida wrote:
Hi Marina,
Thanks for posting updates and information... we've moved from SGE
Nicki Gray wrote:
Hello
When trying to logout from our local instance of Galaxy I get the
error message
This link may not be followed from within Galaxy.
and cant log out. I see this using Firefox, Chrome and Camino
How do I fix this so I can log out?
Hi Nicki,
Are you using
of universe_wsgi.ini:
host = 0.0.0.0
I hope this helps.
--nate
All the best!
Konrad.
-Original Message-
From: Nate Coraor [mailto:n...@bx.psu.edu]
Sent: 19 January 2011 16:43
To: Paszkiewicz, Konrad
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] API connection
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