Dear Galaxy development team,
I've got a problem using the login function of Galaxy.
So I downloaded a copy of Galaxy distribution and installed it on a local
machine, then I installed PostgreSQL on this machine and made the necessary
changes to the universe_wsgi.ini file and Galaxy is able to
Use qrsh instead of qsub to submit the job should help, I believe.
On Tue, Apr 5, 2011 at 10:27 AM, andrew stewart
andrew.c.stew...@gmail.comwrote:
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
Hi,
I created an XML file for a tool. This tool has an Nexus input. When I click
the input field of the web interface for this tool, it shows all kinds of
data that I can select. How do I restrict the list to show only data in
nexus format? I added a line in the registration part and the sniffer
I benchmarked MrBayes 3.1.2 program on my cluster for two cases:
1. use local /tmp for temporary files
2. use the network shared /home/galaxy/galaxy-dist/database/tmp
MrBayes is about 10 times slower for case 2 than for case 1. What I did was
to set the network shared folder as the default but
Hi, Nate,
Yeah, I've already solved the issue, basically used the -e parameter as you
mentioned here. I think the documentation should be corrected.
Thanks,
Luobin
On Tue, Aug 16, 2011 at 12:53 PM, Nate Coraor n...@bx.psu.edu wrote:
Luobin Yang wrote:
Hi,
I am trying to scramble
Hi,
Has anyone set up ProFTPd successfully on Ubuntu 10.04 to enable FTP upload
on Galaxy? I followed the instructions on this link (
http://wiki.g2.bx.psu.edu/Admin/Config/Upload%20via%20FTP) but it doesn't
work.
Thanks,
Luobin
___
Please
://bitbucket.org/afgane/mi-deployment/src/d894af37a83b/mi_fabfile.py#cl-442
(also take a look at the _required_packages method and _setup_users method
because some additional configuration is done there).
Hope this helps,
Enis
On Mon, Sep 12, 2011 at 8:05 PM, Luobin Yang yangl...@isu.edu wrote:
Hi
I have never setup a Galaxy instance fronting multiple clusters, but it's
something I would like to explore. I have a dedicated cluster to run Galaxy
jobs and I've got another a shared cluster to which I hope Galaxy can assign
jobs when the dedicated cluster is too busy.
From my understanding of
Hi,
Recently I moved my locally installed Galaxy from a local hard drive to an
NFS mounted hard drive, when I run some tools, I go the following error from
the log file:
Job output not returned by PBS: the output datasets were deleted while the
job was running, the job was manually dequeued or
: jdu...@illumina.com
** **
*From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto:
galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Luobin Yang
*Sent:* Monday, October 17, 2011 10:31 AM
*To:* galaxy-dev@lists.bx.psu.edu
*Subject:* [galaxy-dev] What's causing this error?
** **
Hi
Hi all,
I configured Sample Tracking System in Galaxy to transfer datasets from a
sequencer to data libraries, however, after I selected the datasets to be
transferred on the sequencer and clicked Transfer button, the transfer
status has been in queue forever.
I didn't find any error message in
( 994debf9f6ab02b9912262b0bd04c784 ) specified,
unable to decode
2012-02-17 09:28:37,928 - datatx_7318 - Setting status Complete for
dataset All of sample 17
Luobin
On Thu, Feb 16, 2012 at 7:58 PM, Luobin Yang yangl...@isu.edu wrote:
Hi all,
I configured Sample Tracking System in Galaxy to transfer datasets from
Hi, all,
Since megablast has been replaced by blastn in newer NCBI BLAST tools, I am
wondering if there is an update on megablast web interface and wrapper in
Galaxy?
Thanks,
Luobin
___
Please keep all replies on the list by using reply all
it looks like the only solution at the moment is to have both NCBI NCBI+
and an old version of BLAST.
Thanks,
Luobin
On Fri, Mar 23, 2012 at 10:55 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Fri, Mar 23, 2012 at 4:36 PM, Luobin Yang yangl...@isu.edu wrote:
I've noticed these wrappers
I've got the same problem and when I looked at the data_transfer.log, I saw
the following message:
2012-03-01 15:12:27,338 - datatx_13870 -
(u'9c17d84742cd2acb63d88b5bd41d968f', u'
http://xxx.xxx.xxx.xxx/api/samples/2d9035b3fc152403',
{'sample_dataset_ids': ['a799d38679e985db',
Hi,
I upgraded Galaxy to the latest version using the command: hg pull -u,
then when I run sh run.sh I got the following error messages:
Initializing openid_conf.xml from openid_conf.xml.sample
Initializing tool-data/bowtie2_indices.loc from bowtie2_indices.loc.sample
Some eggs are out of date,
Hi,
After I update galaxy-dist to the latest version, I got the following error
message when I run run.sh command:
galaxy.tool_shed.tool_shed_registry DEBUG 2012-06-01 09:57:15,503 Loaded
reference to tool shed: Galaxy test tool shed
Traceback (most recent call last):
File
From: Leandro Hermida soft...@leandrohermida.com
To: Luobin Yang yangl...@isu.edu
Cc: Galaxy Dev galaxy-...@bx.psu.edu
Subject: Re: [galaxy-dev] Sample tracking data transfer hangs in
queue forever
Message-ID:
caohzmpj67udrqbhfchgyxnrxsm3qcy1c7jna1kr0ajbnkek
can certainly get together to look at this.
Greg Von Kuster
On Jul 9, 2012, at 1:24 PM, Luobin Yang wrote:
Hi, Greg,
I've still got issues after I downloaded the latest version from the dist
repository. So after I selected the datasets that I would like to transfer
from the sequencer
not
able to fully test this fix though, so if you can let me know if problems
still exist when you get a chance to test it, I'll look further into the
problem after the GCC. Sorry for the inconvenience this has caused.
Thanks ver much!
Greg Von Kuster
On Jul 12, 2012, at 1:07 PM, Luobin Yang
Thanks for the link, Scott, I've confirmed that setting the job runner as
pbs://machine.name/queue.name/-l nodes=n:ppn=m -c enabled/ in universe_wsgi
does not work.
Luobin
On Mon, Nov 5, 2012 at 10:30 AM, Scott McManus scottmcma...@gatech.eduwrote:
I recommend checking out John Chilton's
Hi, guys,
Is it possible to purge some datasets in a history without purging the
whole history?
Thanks,
Luobin
___
Please keep all replies on the list by using reply all
in your mail client. To manage your subscriptions to this
and other
Hi, guys,
I noticed that set_metadata.sh is not in the tools folder as other tools.
Can I set a tool runner for set_metadata.sh so that I can use specific
resources (like specific compute node in the cluster) to run
set_metadata.sh?
Thanks,
Luobin
Hi, Nate,
Thanks for reply. Is it a standalone job that's dispatched when the edit
attribute page is saved?
Thanks,
Luobin
On Mon, Nov 12, 2012 at 12:23 PM, Nate Coraor n...@bx.psu.edu wrote:
On Nov 12, 2012, at 12:38 PM, Luobin Yang wrote:
Hi, guys,
I noticed that set_metadata.sh
Hi, Galaxy developers,
My python version is 2.6.3 and I would like to upgrade it to 2.7.3. So is
there anything that we need to on Galaxy after Python is upgraded to a new
version?
Thanks,
Luobin
___
Please keep all replies on the list by
Hi,
When I run a job in my locally installed Galaxy, there is always an error
message showing in the log file:
Error opening galaxy.json file: [Errno 2] No such file or directory:
'/home/galaxy/galaxy-dist/database/job_working_directory/005/5797/galaxy.json
Any clue how to get rid of it?
Hi,
I checked out a refresh copy of latest galaxy-dist, but I found the
following error in the log file after I ran Galaxy:
galaxy.jobs.handler ERROR 2013-01-27 10:10:19,168 Job runner is not
loadable: galaxy.jobs.runners.lwr
Traceback (most recent call last):
File
Hi,
The list of users is not sorted when I try to impersonate a user, this is
very inconvenient because of the large number of users in the system, is
there a quick way to have users sorted ?
Thanks,
Luobin
___
Please keep all replies on
Hi,
I have a 'select' tag in a tool's XML file, I would like to have a default
option, which is choosing nothing. So the drop down menu of the web
interface will be empty and when a user clicks the drop down menu, the list
contains an empty entry with other options. So I basically have an option
I've got fix for this, add the following line between line 690 and line 691
in lib/galaxy/webapps/galaxy/controllers/admin.py :
emails.sort()
Thanks,
Luobin
On Tue, Jan 29, 2013 at 5:05 PM, Luobin Yang yangl...@isu.edu wrote:
Hi,
The list of users is not sorted when I try to impersonate
Hi, Galaxy developers,
I do not see a web interface for psi-blast in NCBI BLAST+ in the tool shed.
Does it have one?
Thanks,
Luobin
___
Please keep all replies on the list by using reply all
in your mail client. To manage your
Hi, Peter,
I mean the web interface for psiblast on Galaxy system, not the web
interface at NCBI.
Thanks,
Luobin
On Mon, Feb 4, 2013 at 10:30 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Mon, Feb 4, 2013 at 5:20 PM, Luobin Yang yangl...@isu.edu wrote:
Hi, Galaxy developers,
I do
...@googlemail.comwrote:
On Mon, Feb 4, 2013 at 5:20 PM, Luobin Yang yangl...@isu.edu wrote:
Hi, Galaxy developers,
I do not see a web interface for psi-blast in NCBI BLAST+ in the tool
shed.
Does it have one?
Thanks,
Luobin
If you are asking about the ncbi_blast_plus suite in the Tool
...@googlemail.comwrote:
On Mon, Feb 4, 2013 at 5:43 PM, Luobin Yang yangl...@isu.edu wrote:
Hi, Peter,
What difficulties did you see to include psi-blast and phi-blast when you
were working on the other programs in the NCBI+ suite? I would be
interested
in creating a tool configuration
...@googlemail.com
wrote:
On Monday, February 4, 2013, Luobin Yang wrote:
Hi, Peter,
Thanks for pointing them out!
The phi-blast and psi-blast actually share the same binary, both use the
psiblast program in the NCBI BLAST+ tools. When the option -phi_pattern
is
used, then it does phi
Hi, Galaxy developers,
I would like to have the parameters on the web interface to be packed into
sections for a tool. Is there a way to do this? There is a page tag, but
the document says we should avoid using it. Also there is no replacement
tag for page. The problem using the page tag is that
Hi,
I tried the pcx and ps formats, but the browser just downloads these kinds
of files instead rendering them in the Galaxy window... It seems png and
pdf files can be rendered in the Galaxy windows. How can I make Galaxy
display other image formats like ps and pcx?
Thanks,
Luobin
Galaxy supplies the required mimetype, the user has
to download the PDF and open it by hand.
On Fri, Feb 8, 2013 at 10:16 AM, Peter Cock p.j.a.c...@googlemail.comwrote:
On Thu, Feb 7, 2013 at 9:41 PM, Luobin Yang yangl...@isu.edu wrote:
Hi,
I tried the pcx and ps formats, but the browser
Hi, guys,
Recently I found the Upload File tool under the Get Data category runs
forever on my locally installed Galaxy system. It worked fine for a long
time, but now it's not working anymore. Have you guys experienced similar
things?
Thanks,
Luobin
This is strange: when I submit a job through the computers on campus to my
locally installed Galaxy, the job finishes without no problem, but when I
submit the same job through a computer off-campus, the job generates empty
or 'no peek' output. What's causing the problem?
Luobin
40 matches
Mail list logo
