On Dec 20, 2011, at 1:09 PM, Bicak, Mesude wrote:
Dear Galaxy Developers,
We work in Professor Dawn Field's group (Molecular Evolution and
Bioinformatics Research Group) at the NERC Environmental Bioinformatics
Centre (NEBC) of the Centre for Ecology and Hydrology (CEH) Research
On Dec 22, 2011, at 11:13 AM, Liang Zhang wrote:
Dear Galaxy team:
I was trying to use the Get Data – Upload File tool
yesterday. I uploaded all files through FTP. Then selected them in “Files
uploaded via FTP”, selected “auto-detect” + ”Mouse July 2007 (NCBI37/mm9)
I set up my Apache server to act as a proxy server based on the docs at
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
My pages aren't loading correctly and I discovered that since I have galaxy
installed as its own user, the apache user account does not have access to
the galaxy files. I
Your database is not cleanly dropped when you start up your Galaxy server -
notice all of the migration scripts that fail because table columns, etc
already exist. Here's an example:
0012_user_address DEBUG 2011-12-14 15:15:12,085 Adding column 'deleted' to
request_type table failed:
On Dec 29, 2011, at 12:15 AM, Cai Shaojiang wrote:
Dear friends,
We are trying to install galaxy on the server (ubuntu 11), just by
following the steps on the page Get Galaxy: Galaxy Download and
Installation of galaxy wiki. But when we start running it, it shows
the following error
On Dec 29, 2011, at 4:29 PM, Ryan Golhar wrote:
Hi - I've just finished installing a ROCKS 5.4.3 cluster and am now adding
Galaxy to it. We are using torque instead of SGE. I see the Wiki docs at
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Cluster state I need to
scramble
Hi all - I'm setting up Galaxy under Apache and following the guide for a
production environment. I've got the proxy server running properly and am
now setting up load balancing. I currently start galaxy (for testing)
using 'sh run.sh --reload' so I can stop galaxy using Ctrl-C.
I'm following
On Jan 3, 2012, at 1:19 PM, Ryan wrote:
Hi all - I'm setting up Galaxy under Apache and following the guide for a
production environment. I've got the proxy server running properly and am
now setting up load balancing. I currently start galaxy (for testing) using
'sh run.sh --reload' so
On Dec 6, 2011, at 2:16 PM, Mary Anne Alliegro wrote:
No, it is still reads over 120GB yet the usage is only 26%
Hi Mary Anne,
Sorry I didn't get back to you sooner. Your usage is currently ~75GB. The
difference before may have been due to some other data in your account which
was not
On Dec 10, 2011, at 8:47 AM, Xuebing Wu wrote:
Hi,
I'm wondering if there is a way to disable the error detection (output
showing red). I was adding some tools to a local Galaxy server. Some
of the tool's stdout were directed to a file. The tool ran without an
error, but Galaxy treated
On Dec 15, 2011, at 4:05 PM, weihong yan wrote:
I recently installed galaxy program on our Linux server and it is going to be
used for analyzing high-throuput sequencing data. I tried to upload a
dataset (a bed format file) from local computer to galaxy server, but no
success. The
On Dec 15, 2011, at 4:39 PM, weihong yan wrote:
Galaxy was configured with Apache as proxy server. The uploaded file size is
very small. The message from paster.log related with it is
POST /False?nginx_redir=/tool_runner/index HTTP/1.1 200 -
On Dec 20, 2011, at 12:19 AM, Le-Shin Wu wrote:
Thanks a million, Nate. I was able to submit my PBS job though galaxy. But I
got another problem once the PBS job is finished.
I submit a bowtie alignment testing job to our cluster by using PBS runner
through galaxy. But I always got an
On Dec 20, 2011, at 5:04 AM, Cittaro Davide wrote:
Hi developers, I have a question that may be an OT, but since galaxy can work
in a clustered environment withh queueing system, I'll try to ask here.
Is there anibody here who copies data in a local temporary directory before
performing any
On Dec 20, 2011, at 8:48 AM, Marc Bras wrote:
Hi,
We have a Galaxy server in production and I have a problem when I want to
download a huge file with HTTP URL.
Galaxy starts well to download my file, but Galaxy writes this file in /
tmp directory.
Is it possible to change this
Hi all - I had this problem once before with a previous installation, and
thought it was fixed, but I'm seeing it again and not sure its related.
I have Galaxy running with a Proxy server on apache to get /galaxy instead
of using port 8080. I've disabled load balancing and running everything in
On Dec 20, 2011, at 6:16 PM, Langhorst, Brad wrote:
I'm working on unpacking a zip file into multiple datasets.
I think this is the code path
Upload.py
UploadToolAction
upload_common.py:
get_uploaded_datesets
new_upload
new_history_upload or new_library_upload
Then a job gets
Hi,
I'm executing a R script via Python's os.system() (using Rscript executable
which allow executing R script in the command line). This script makes use
of library that will attempt to load up Tcl/Tk interface. Though I don't
see anything even if I'm running the commands on Windows interactive
On Tue, Jan 3, 2012 at 4:21 PM, Ryan ngsbioinformat...@gmail.com wrote:
Hi all - I had this problem once before with a previous installation, and
thought it was fixed, but I'm seeing it again and not sure its related.
I have Galaxy running with a Proxy server on apache to get /galaxy instead
On Tue, Jan 3, 2012 at 4:21 PM, Ryan ngsbioinformat...@gmail.com wrote:
Hi all - I had this problem once before with a previous installation, and
thought it was fixed, but I'm seeing it again and not sure its related.
I have Galaxy running with a Proxy server on apache to get /galaxy
Hello all,
I am trying to configure an Asynchronous tool (I can get it to work
synchronously).
My configuration looks something like this for the tool:
?xml version=1.0?
tool name=mytoolname id=myunique_tool_id_1 tool_type=data_source_async
descriptionmytool description/description
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