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
__
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
__
ng to get working -
> until then, even when 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 wrote:
>
>> On Thu, Feb 7, 2013 at 9:41 PM, Luobin Yang wrote:
>> > Hi,
>
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
__
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 tag, but
the document says we should avoid using it. Also there is no replacement
tag for . The problem using the tag is that there seems
m
> > 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
:
> On Mon, Feb 4, 2013 at 5:43 PM, Luobin Yang 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 conf
On Mon, Feb 4, 2013 at 5:20 PM, Luobin Yang 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 n
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 wrote:
> On Mon, Feb 4, 2013 at 5:20 PM, Luobin Yang wrote:
> > Hi, Galaxy developers,
> >
> > I do not see a
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 subscriptio
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 wrote:
> Hi,
>
> The list of users is not sorted when I try to impersonate a
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
t
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 the
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 "/home/galaxy/galaxy-dist/lib
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?
Thanks
xy/galaxy-dist/lib/galaxy/datatypes/wsf.pyc
On Wed, Jan 23, 2013 at 3:48 PM, Luobin Yang wrote:
> Hi, Nate,
>
> It seems fetch_eggs.py does not run correctly on the compute node, which
> runs Ubuntu 12.04.1 LTS and Python 2.7.3. After I ran "python
> scripts/fetch_eggs.py&q
_conflict
r = pkg_resources.working_set.resolve( ( dist.as_requirement(), ), env,
egg.fetch )
File "/usr/lib/python2.7/dist-packages/pkg_resources.py", line 584, in
resolve
raise DistributionNotFound(req)
pkg_resources.DistributionNotFound: docutils==0.7
On Wed, Jan 23, 2013 at
Hi,
I ran into this error and I found the following thread discussing the
problem, interestingly, for my system, the computer node runs the same
Python version as the head node, but with a newer OS version, but it also
generates this error. Does this mean the Galaxy system requires the
computer no
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 us
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 wrote:
> On Nov 12, 2012, at 12:38 PM, Luobin Yang wrote:
>
> > Hi, guys,
> >
> > I
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, guys,
Is it possible to purge some datasets in a history without purging the
whole history?
Thanks,
Luobin
___
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in your mail client. To manage your subscriptions to this
and other G
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 wrote:
> I recommend checking out John Chilton's dynamic job runner first:
>
Hi, guys,
I would like to enable checkpoint and restart for some galaxy jobs. In
order to do that, I need to add "-c enabled" option when using "qsub" to
submit a job. What files should I change to add this option? I am using
Torque PBS job runner.
Thanks,
Luobin
_
on. I am 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 Kust
few weeks is very hectic. If you'll be at either ISMB or the
> GCC, we 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
mply with the request since it is either
> malformed or otherwise incorrect."
> >
> > Does anyone have a solution for this?
> >
> > Thanks
> > Emily
> >
> >
> >
> > --
> >
> > Message: 17
> > Date: Wed, 28 Mar 2012 13:15:47 +0200
> > From
status
>
> And then finally:
>
> hg diff
>
>
> Thanks,
>
> Greg Von Kuster
>
>
> On Jun 1, 2012, at 12:06 PM, Luobin Yang wrote:
>
> Hi,
>
> After I update galaxy-dist to the latest version, I got the following
> error message when I run run.sh comma
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 "/home/galaxy/galaxy-
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 dat
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', '33b43b4e7093c91f']
So 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 wrote:
> On Fri, Mar 23, 2012 at 4:36 PM, Luobin Yang wrote:
> > I've noticed these wrappers for BLAST+. I actually wa
I've noticed these wrappers for BLAST+. I actually was talking about the
megablast tool under NGS Mapping section...
Thanks,
Luobin
On Fri, Mar 23, 2012 at 10:27 AM, Peter Cock wrote:
> On Fri, Mar 23, 2012 at 4:22 PM, Luobin Yang wrote:
> > Hi, all,
> >
> > Since m
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
I noticed that mrFAST is listed in the Galaxy tool shed, but the
downloadable files are the source code of mrFAST program itself instead of
the web interface XML file. Does mrFAST have a web interface definition
file and a possible wrapper program?
Thanks,
Luobin
__
yFolder id ( 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 wrote:
> Hi all,
>
> I configured Sample Trac
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
Hi,
I have a local instance of Galaxy, but I found there is no "Display at UCSC
Main" link for some datasets that can be viewed in GeneTrack or displayed
by Ensemble, what has been wrong?
Thanks,
Luobin
___
Please keep all replies on the lis
> Sr. Staff Software Engineer
> Illumina, Inc.
> *9885 Towne Centre Drive
> San Diego, CA 92121
> Tel: 858-736-3584
> E-mail: jdu...@illumina.com****
>
> ** **
>
> *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto:
> galaxy-dev-boun...@lists.bx.psu.edu] *On Beh
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 th
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
t;>
>> The method is available here:
>> https://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).
>&g
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 k
On Wed, Aug 17, 2011 at 2:59 AM, Roman Valls wrote:
> On 2011-08-16 23:49, Luobin Yang wrote:
> > Hi, Nate,
> >
> > On Tue, Aug 16, 2011 at 12:38 PM, Nate Coraor > <mailto:n...@bx.psu.edu>> wrote:
> >
> > Hi Luobin,
> >
> > Sorr
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 wrote:
> Luobin Yang wrote:
> > Hi,
> >
> > I am trying
to come up with
> additional ideas than what we on the Galaxy Team come up with.
>
> Please see my responses inline below.
>
> Luobin Yang wrote:
> > Hi,
> >
> > Thanks for Martin Dahlo's excellent blog (
> > http://mdahlo.blogspot.com/2011/06/galaxy-on-uppm
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 i
since this has happen to me several
> times when adding a new datatype). Have you double checked your tool
> definition file?
>
>
> Regards, Hans
>
>
>
> On 07/22/2011 07:52 AM, Luobin Yang wrote:
>
>> Hi,
>>
>> I created an XML file for a tool.
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 p
Hi,
The "reload a tool's configuration" menu avoids restarting Galaxy system
when a tool's web interface changed, but it doesn't seem to reload the
".loc" files that a tool's XML file uses. I am wondering if it's possible to
reload the ".loc" file also?
Thanks,
Luobin
Use qrsh instead of qsub to submit the job should help, I believe.
On Tue, Apr 5, 2011 at 10:27 AM, 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 submi
logout page, then it is being caused by the bug
> above, and will be fixed in the next stable release of Galaxy.
>
> --nate
>
> >
> > Thanks.
> >
> > Best regards,
> > Chee Seng
> >
> > From: galaxy-dev-boun...@lists.bx.psu.edu [mailt
y visiting a different page or click on "Analyze Data", then click on log
> in. Once I navigated off the login page then came back, I was able to
> login.
>
> Ryan
>
>
> On 3/11/11 2:17 PM, Luobin Yang wrote:
>
>> Dear Galaxy development team,
>>
>> I
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 th
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