On May 20, 2013, at 3:08 PM, Nate Coraor wrote:
> On May 20, 2013, at 3:31 PM, Fields, Christopher J wrote:
>
>> On May 20, 2013, at 9:45 AM, Nate Coraor
>> wrote:
>>
>>> On May 19, 2013, at 11:41 PM, Fields, Christopher J wrote:
>>>
>>>&
On May 21, 2013, at 2:13 PM, Christopher Fields
wrote:
> On May 20, 2013, at 3:08 PM, Nate Coraor wrote:
>> ...
>> Hi Chris,
>>
>> We're disconnecting under all normal conditions and most error conditions -
>> it looks like only a few conditions would not properly disconnect:
>>
>> - If pbs_
On May 20, 2013, at 9:45 AM, Nate Coraor
wrote:
> On May 19, 2013, at 11:41 PM, Fields, Christopher J wrote:
>
>> I've been seeing this error popping up quite a bit recently (we're using
>> Torque 3.0.5), which is giving a general 'cluster
I've been seeing this error popping up quite a bit recently (we're using Torque
3.0.5), which is giving a general 'cluster failure' Galaxy error on jobs:
galaxy.jobs.runners.pbs WARNING 2013-05-19 18:56:44,073 (10588) pbs_submit
failed (try 1/5), PBS error 15033: No free connections
This ju
I saw this same problem with our upload1 set to run on the cluster (it had
worked properly a few months prior). I found out that the cluster sysadmins
had set the nodes for local access only (no web access), direct file uploads
and FTP to local disk worked but URL-based uploads did not.
The
The user impersonation feature doesn't work with external authentication.
There is a bug report on this:
https://trello.com/c/zwqNwflD
chris
On Dec 13, 2012, at 10:01 AM, greg wrote:
> The problem is I disabled the logout button in universe.wsgi (I think)
>
> (I believe I did that to make i
Older versions of GATK can be grabbed from Github:
https://github.com/broadgsa/gatk/tags
Not sure if they have an official 'older version' download site.
chris
On Dec 13, 2012, at 9:51 AM, yg...@cpdr.org wrote:
> Hi,
>
> Could anyone give me some suggestions about that?
> Thanks very much.
On Oct 19, 2012, at 9:35 AM, Carlos Borroto wrote:
> On Fri, Oct 19, 2012 at 12:00 AM, Fields, Christopher J
> wrote:
>>
>> My local one is set up like this and it works (for augustus):
>>
>>toolshed.g2.bx.psu.edu/repos/bjoern-gruening/augustus/augustus/0.1 =
Yes, have to agree there, an error would be more informative.
chris
On Oct 20, 2012, at 2:38 PM, Shane Sturrock wrote:
> That would certainly have saved me a fair bit of time since the only
> indication I got was an empty set of quotes in the error log. I always feel
> like tabs aren't the b
On Oct 4, 2012, at 3:11 PM, Peter Cock wrote:
> On Thu, Oct 4, 2012 at 8:56 PM, Shane Sturrock wrote:
>> I've just been setting up our internal galaxy server and following
>> the instructions to get the NCBI BLAST+ tool working but I kept
>> getting stuck with it passing -db "" in rather than th
On Oct 17, 2012, at 3:53 PM, Carlos Borroto wrote:
> On Mon, Oct 15, 2012 at 11:49 AM, Liisa Koski wrote:
>> Hello,
>> I've installed a tool to my local Galaxy installation via my local ToolShed.
>> I would like to run this tool locally, and not have it submitted to the
>> grid.
>>
>> I have tr
I had an odd error with wigToBigWig that I tracked back to the *.len files
generated by the updateucsc.sh script. With my last UCSC update, a majority of
the assemblies have this as the single line:
but others, like Zea_mays_B73_RefGen_v2, are fine. Rerunning this gives the
same pro
On Sep 15, 2012, at 11:05 PM, Jeremy Goecks wrote:
>> is there a way to determine whether Trackster is the cause?
>
> The only place where Trackster caches data is in the SummaryTreeDataProvider.
> In galaxy-central, the relevant line is 709 in
> lib/galaxy/visualization/genome/data_providers
the first time
`round).
chris
On Sep 16, 2012, at 1:34 PM, James Taylor wrote:
>
>
> On Sunday, September 16, 2012, Fields, Christopher J wrote:
> This seems to correspond with what I have tried; I attempter setting
> log_destination in the config file (as James suggested) an
de with hg updates.
chris
On Sep 12, 2012, at 2:32 PM, Nate Coraor wrote:
> On Sep 12, 2012, at 1:09 PM, Fields, Christopher J wrote:
>
>> Simple question: is there a way within universe_wsgi.ini to point to a
>> specific location where Galaxy log (and possibly PID) files can be
We're seeing an odd issue that seems to be related to Trackster's caching of
track information, mainly that memory in the web server processes increases.
It appears that tracks are being cached in memory per web process.
If I create a new visualization (and monitor our web processed via top) we
Simple question: is there a way within universe_wsgi.ini to point to a specific
location where Galaxy log (and possibly PID) files can be dropped? I've
searched for this but couldn't find an answer beyond locally modifying run.sh,
but it's entirely possible I'm missing something obvious.
We wa
The docs about that are here:
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling
I am working on combining our separate ini files myself, but ran into some odd
problems with cluster job submission that weren't present with the original
split files (e.g. the combi
pdates?
>
> Cheers,
> Jelle
>
>
> On Mon, Jul 30, 2012 at 7:03 PM, Fields, Christopher J
> wrote:
>> I'm seeing a possible latency issue or race condition when starting Galaxy
>> after the latest hg upgrade (July 20) from galaxy-dist; the prior upgrade
&g
I'm seeing a possible latency issue or race condition when starting Galaxy
after the latest hg upgrade (July 20) from galaxy-dist; the prior upgrade
doesn't have this problem. We have small setup with one job manager/runner and
two web front-ends for testing load balancing:
…from universe_wsgi
On Jun 11, 2012, at 9:10 AM, Nate Coraor wrote:
> On Jun 10, 2012, at 8:56 PM, Ciara Ledero wrote:
>
>> Hi all,
>>
>> So I was not able to configure Galaxy immediately after this post of mine
>> due to the tasks that I first needed to do. Looking back, I forgot to ask
>> this question:
>>
>>
On Jun 8, 2012, at 8:42 AM, Peter Cock wrote:
> On Fri, Jun 8, 2012 at 2:38 PM, Raj Ayyampalayam wrote:
>> Hello,
>>
>> I am interested in this "local upload file" tool. Can you please send the
>> files to me as well.
>>
>> Thanks.
>> -Raj
>
> This seems a potentially very useful tool, so putt
On May 10, 2012, at 11:02 AM, Nate Coraor wrote:
> On May 3, 2012, at 3:42 PM, Dorset, Daniel C wrote:
>
>> I have had Galaxy running on a local BAS, and after success with that we’re
>> ready to create an instance on our local cluster computing service. The
>> local cluster uses PBS/Torque.
>>
We are using PBS locally and had our cluster admin set this up, but I think the
same principle applies across most job runners/mgrs. As Peter mentioned, there
should be a way for cluster admin to add your server as an allowed submitting
host, the PBS variant is here:
http://www.clusterre
We've also started a local deployment for University of Illinois
Urbana-Champaign. So I would be interested in participating.
Chris
On Apr 27, 2012, at 2:32 PM, "David Hoover" wrote:
> Not a bad idea. Most of the conversations on this list are very limited and
> detailed in scope, dealing w
You can change the default location of tmp files by modifying the environment;
we ran into this with samtools directly dumping temp sort files to a local
node, causing the job to shut down. Setting TMPDIR worked for me.
chris
On Mar 11, 2012, at 5:10 PM, Dorset, Daniel C wrote:
> Hi Luciano,
This seems to fall within the recent discussion of map/reduce operators for
workflows, e.g. breaking large jobs up for embarrassingly parallel tasks, then
merging them back at some later point. Dannon mentioned some basic
functionality does exist within Galaxy to do this, but it's at an early s
Yes, we are using this locally (sftp and scp). Basically follow the same rules
as for FTP on the wiki, but leave out the ProFTP setup; this was per Nate's
instructions, whom I believe is to change the FTP-specific documentation at
some point.
Basically, any mechanism that transfers data to t
trac/pbs-drmaa
>
> And it works now! :D
>
> Have a great weekend,
> L-A
>
>
> Le 17/02/2012 17:07, Fields, Christopher J a écrit :
>> If they used a package install, I think the DRMAA libs for torque are
>> normally separate. For instance:
>>
>> htt
This was recently brought up in a related thread by Nate, the code is in a pull
request on bitbucket. Changing the subject to see if that rings any additional
bells…
Here's the original post by John Chilton and link to the fork:
http://galaxy-development-list-archive.2308389.n4.nabble.com/Defi
If they used a package install, I think the DRMAA libs for torque are normally
separate. For instance:
http://pkgs.org/download/torque-drmaa
If going from source, you can enable DRMAA compilation with --enable-drmaa; I
don't recall if that is on by default (I don't think it is).
chris
On Feb
On Feb 16, 2012, at 12:24 PM, Peter Cock wrote:
> On Thu, Feb 16, 2012 at 4:28 PM, Peter Cock wrote:
>> Hi Dan,
>>
>> I think I need a little more advice - what is the role of the script
>> scripts/extract_dataset_part.py and the JSON files created
>> when splitting FASTQ files in lib/galaxy/dat
On Feb 16, 2012, at 4:47 AM, Peter Cock wrote:
> On Wed, Feb 15, 2012 at 6:07 PM, Dannon Baker wrote:
>> Good luck, let me know how it goes, and again - contributions are certainly
>> welcome :)
>
> I think I found the first bug, method split in
> lib/galaxy/datatypes/sequence.py
> for class Se
Ah, was just about to ask about this as well, nice to know something is already
in place (as experimental as it might be). Thanks Dannon!
chris
On Feb 15, 2012, at 11:08 AM, Dannon Baker wrote:
> It's definitely an experimental feature at this point, and there's no wiki,
> but basic support fo
On Feb 13, 2012, at 9:45 AM, Nate Coraor wrote:
> On Feb 8, 2012, at 9:32 PM, Fields, Christopher J wrote:
>
>> 'samtools sort' seems to be running on our server end as well (not on the
>> cluster). I may look into it a bit more myself. Snapshot of top off our
Forgot to add, but this also seems tied to the same problem Ryan's describing.
IIRC Galaxy also runs 'samtools sort' after certain jobs, correct?
chris
On Feb 8, 2012, at 8:32 PM, Fields, Christopher J wrote:
> 'samtools sort' seems to be running on our se
'samtools sort' seems to be running on our server end as well (not on the
cluster). I may look into it a bit more myself. Snapshot of top off our
server (you can see our local runner as well):
PID USER PR NI VIRT RES SHR S %CPU %MEMTIME+ COMMAND
3950 galaxy20
maybe it's tool-specific?
>>
>> chris
>>
>>
>> On Feb 3, 2012, at 1:10 AM, Dannon Baker wrote:
>>
>>> Can you share a workflow that's failing for you on test with me? I just
>>> tried a simple workflow with nothing but an input an
h me? I just
> tried a simple workflow with nothing but an input and FastQC and ran with
> multiple inputs successfully.
>
> Thanks!
>
> Dannon
>
>
> On Feb 2, 2012, at 11:15 PM, Fields, Christopher J wrote:
>
>> Just filed as Issue #714 on bitbucket. I noti
Just filed as Issue #714 on bitbucket. I noticed that multiple input seems to
be broken on workflows when selecting more that one file (a single file works).
This is happening on our local instance, using Jan 27 galaxy-dist release, as
well as both main/test.g2.bx.psu.edu Galaxy servers (latte
ate Coraor wrote:
> On Jan 19, 2012, at 12:57 AM, Fields, Christopher J wrote:
>
>> Just to add for the list, nate mentioned on IRC that running tests on an
>> external server likely doesn't work at the moment but that
>> ./scripts/functional_tests.py may have som
David,
This is the approach recommended on the wiki for performance:
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
Would be nice if your alternative approach using virtual hosts were similarly
documented.
chris
On Jan 19, 2012, at 10:01 AM, David Hoover wrote:
> Why do you need to
We also ran into this. Our local server configuration was case-sensitive and
the LDAP uid key was converted to upper-case, so we used:
RequestHeader set REMOTE_USER %{AUTHENTICATE_UID}e
which fixed the problem. We found the solution by searching for
'AUTHENTICATE_uid', it appears to be a re
Just to add for the list, nate mentioned on IRC that running tests on an
external server likely doesn't work at the moment but that
./scripts/functional_tests.py may have something to work with via environment
variables.
chris
On Jan 18, 2012, at 8:03 PM, Fields, Christopher J wrote:
&
ne.
>
> %sh run_functional_tests.sh
>
> There are several options you can use as well.
>
> Greg
>
> On Jan 18, 2012, at 4:38 PM, Fields, Christopher J wrote:
>
>> I have been following the basic protocol for running remote tests on a
>> Galaxy server (in this case, our
I have been following the basic protocol for running remote tests on a Galaxy
server (in this case, our local one) using:
http://wiki.g2.bx.psu.edu/Admin/Running%20Tests
>From reading this, I assume the tests are to be run from the galaxy root
>directory, like so:
GALAXY_TEST_EXTERNAL=1 GAL
Do you mean this (In universe_wsgi.ini)?
...
# Debug enables access to various config options useful for development and
# debugging: use_lint, use_profile, use_printdebug and use_interactive. It
# also causes the files used by PBS/SGE (submission script, output, and error)
# to remain on disk af
We are anticipating a similar issue and decided it would be easier to just have
separate VMs where possible. I know this isn't always possible, but it is a
very easy way to both manage multiple galaxy instances and keep the various
galaxy instances completely separate.
Chris
On Dec 22, 2011,
The first option (wrapper) also gives one the opportunity to actually check for
errors.
Chris
On Dec 22, 2011, at 2:21 AM, "Mikel Egaña Aranguren" wrote:
> Hi;
>
> My interpretation is that your BioJava tool is sending normal information to
> stderr, and Galaxy interprets it as an error. The
On Nov 29, 2011, at 3:13 AM, Peter Cock wrote:
> On Monday, November 28, 2011, Joseph Hargitai
> wrote:
> > Ed,
> >
> > we had the classic goof on our cluster with this. 4 nodes could not see the
> > /home/galaxy folder due to a missing entry in /etc/fstab. When the jobs hit
> > those nodes (w
Try http://test.g2.bx.psu.edu/
chris
On Nov 15, 2011, at 3:13 PM, Yan Luo wrote:
> Hi, Dannon,
>
> Thanks for your response. I just tried "test.bx.psu.edu", but it was not
> available. Could you please double check the address?
>
> Looking forward to hearing from you.
>
> Thanks,
>
> Yan
>
> If there's a desire for tightened security, I would be happy to review
> and accept any work done on that. =)
>
> --nate
That is a possibility, we have initially talked with a few of the myproxy folks
here re: security concerns and possible solutions for user job submissions
011, at 4:59 PM, Fields, Christopher J wrote:
> I recall at the Galaxy conf there were questions on how secure this is
> (having the 'galaxy' user submit jobs as someone else). This would involve
> switching users on the cluster or would require user login information,
> correc
I recall at the Galaxy conf there were questions on how secure this is (having
the 'galaxy' user submit jobs as someone else). This would involve switching
users on the cluster or would require user login information, correct?
The way we planned on working around this was to just specify a user
On Oct 24, 2011, at 2:57 AM, Peter Cock wrote:
> On Mon, Oct 24, 2011 at 4:53 AM, John Chilton wrote:
>> Hello All,
>>
>> This is more of a general policy question. The head of our Research
>> Informatics Support Systems group here at the University of Minnesota wants
>> to know how other in
On Oct 19, 2011, at 8:03 AM, Peter Cock wrote:
> On Wed, Oct 19, 2011 at 1:41 PM, Fields, Christopher J
> wrote:
>> On Oct 19, 2011, at 4:33 AM, Peter Cock wrote:
>>
>>> On Wed, Oct 19, 2011 at 10:24 AM, Jeroen Crappé
>>> wrote:
>>>> Dear a
On Oct 19, 2011, at 4:33 AM, Peter Cock wrote:
> On Wed, Oct 19, 2011 at 10:24 AM, Jeroen Crappé
> wrote:
>> Dear all,
>>
>> I have recently installed a local galaxy on our servers.
>> I could succesfully add a blastable database via the blastdb.loc file.
>> All is working, so no problems regar
The use of (unaligned) BAM for readgroups seems like a good idea. At the very
least it prevents inconsistently hacking this information into the FASTQ
descriptor (a common problem with any simple format).
chris
On Sep 8, 2011, at 1:35 PM, Edward Kirton wrote:
> copied from another thread:
>
On Sep 2, 2011, at 8:02 PM, Peter Cock wrote:
> On Fri, Sep 2, 2011 at 9:27 PM, Fields, Christopher J
> wrote:
>> On Sep 2, 2011, at 3:02 PM, Edward Kirton wrote:
>>
>>>> What, like a BAM file of unaligned reads? Uses gzip compression, and
>>>> tracks
On Sep 2, 2011, at 3:02 PM, Edward Kirton wrote:
>> What, like a BAM file of unaligned reads? Uses gzip compression, and
>> tracks the pairing information explicitly :) Some tools will already take
>> this as an input format, but not all.
>
> ah, yes, precisely. i actually think illumina's pipel
On Sep 2, 2011, at 9:57 AM, Nate Coraor wrote:
> ...
>> Chatting to some of the Galaxy team at BOSC/ISMB 2011
>> there is some support for this internally. Again, there are
>> automated tools to do this.
>>
>>> would anyone be willing to add the appropriate hooks to
>>> the central repository as
61 matches
Mail list logo
