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
John Powell (NIH/CIT) [E] wrote:
>
> Trying to install a local copy of Galaxy for evaluation. Downloaded
> the "stable" version using:
>
> hg clone https://bitbucket.org/galaxy/galaxy-dist
>
> I am installing it on a Centos 5 x86_64 Linux kernel which has
> python 2.4.3 installed. When running
Pieter Neerincx wrote:
>
> Hi John and Nate,
>
> But to make the tool search work in the web interface you'll need Python 2.5
> or higher, so it's probably a better idea to get a newer version of Python
> anyway. (We have Galaxy on two CentOS servers, installed a newer Python in
> addition to
;s startup files
(~/.bash_profile).
--nate
>
> Thanks again...
>
>
> At 09:54 AM 2/9/2011, Nate Coraor wrote:
> >Pieter Neerincx wrote:
> >>
> >> Hi John and Nate,
> >>
> >> But to make the tool search work in the web interface you'll
Hi Yan,
I've moved this discussion to the galaxy-dev list since it pertains to a
local installation of Galaxy.
Responses to your questions follow, in-line.
Yan Luo wrote:
> Dear Sir,
>
> (1)We installed Galaxy, but recently the user can't registered and got the
> following error, how can we fix
Sonali Amonkar wrote:
> Hi,
>
>
> I'm trying to install and run galaxy-dist-8729d2e29b02 on a Linux RHEL 5.5
> box. This machine has no direct access to the Internet. I followed the steps
> listed on the page
> https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Eggs to download the
> egg
phone #? I can call you sometime today, or if you prefer, I can
> give you my phone #.
Unfortunately, we don't have the resources for phone support. We'll be
happy to help via email as much as possible.
--nate
>
> Looking forward to hearing from you.
>
> Best Wishes,
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 Ga
t email.
The second would be to pull our in-development code, but be aware that
this has undergone very little testing at this point. You can pull the
most recent changes with:
% hg pull -u http://bitbucket.org/galaxy/galaxy-central/
--nate
>
>
> Looking forward to hearing
te@weyerbacher% . ./galaxy_env/bin/activate
> nate@weyerbacher% cd galaxy_dist
> nate@weyerbacher% sh run.sh
This should be fine.
--nate
>
>
> ------
>
> Looking forward to hearing from you.
>
> Best Wishes,
>
> Yan
>
>
> On Fri, Feb 11, 2011 at 8:45 AM, Nate Coraor
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 fi
te@weyerbacher% /usr/bin/python2.6 virtualenv.py --no-site-packages
> > galaxy_env
> > New python executable in galaxy_env/bin/python2.6
> >
> > Also creating executable in galaxy_env/bin/python
> > Installing setuptools...done.
> >
> > (c)run the followi
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'
when I check the above folder, I do find the file 'activate'
> >
> > kangtu@dscbc-compute:~/Downloads/galaxy-dist/galaxy_env/bin$ ls
> > activate activate.fish easy_install pip python
> > activate.csh activate_this.py easy_install-2.6 pip-2.6
> >
te
>
> Thanks for your help, I hope it is smooth.
>
> Best Wishes,
>
> Yan
>
> On Fri, Feb 11, 2011 at 10:31 AM, Nate Coraor wrote:
>
> > Yan Luo wrote:
> > > Dear Nate,
> > >
> > > When I run ".
> > /home/kangtu/data/tool
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
Hi John,
This is fantastic, thanks for writing this. I've committed the
Galaxy-side code in 5050:74048a9ab689, so the patch should no longer be
required. I'll try to get something placed on the Cluster page in the
wiki, too.
Thanks,
--nate
John Chilton wrote:
> Hello,
>
> We are looking a
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.pb
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.jo
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:
>
> /home/abc/galaxy/li
Yan Luo wrote:
> Dear Nate,
>
> I have a new problem, last week, I restarted the Galaxy, but it worked well.
> This morning, I found I can't start it from browser, but when I check "ps
> auxwww|grep python", I still find it is running, what is problem?
What happens when you try to connect via a b
assistance.
--nate
>
>
> Any suggestion will be appreciate.
>
> Best Wishes,
>
> Yan
>
>
>
> On Mon, Feb 14, 2011 at 8:43 AM, Nate Coraor wrote:
>
> > Yan Luo wrote:
> > > Dear Nate,
> > >
> > > I have a new problem,
m? Anyway, Galaxy works.
Assuming nothing else has changed, it sounds like your NFS server is
having some performance problems.
--nate
>
> Thanks,
>
> Yan
>
> On Mon, Feb 14, 2011 at 8:49 AM, Nate Coraor wrote:
>
> > Yan Luo wrote:
> > > Dear Nate,
> > >
Sonali Amonkar wrote:
> On further digging, we found that the script is failing in the following part
> of $GALAXY_HOME/lib/galaxy/jobs/runners/pbs.py:
>
> # submit
> galaxy_job_id = job_wrapper.job_id
> log.debug("(%s) submitting file %s" % ( galaxy_job_id, job_file ) )
>
Hi Florent, et. al.,
I've moved the discussion over to galaxy-dev since it pertains to local
instances.
Florent Angly wrote:
>
> Indeed, this workaround works! Thank you.
> I added these lines to the beginning of my run.sh:
> PATH="/opt/local/bin:/opt/local/sbin:$PATH"
> export $PATH
>
Sonali Amonkar wrote:
> Hi Ryan,
> I think you might want to upgrade your Python version. I was facing this
> issue and Python 2.6.6 version fixed it.
It's correct that there's a bug in the current distribution version that
prevents it from running on Python 2.4. However, we have a new release
o
Christian Dreischer wrote:
> Hello community,
>
> I'm new to Galaxy and are currently trying to install a new instance on a
> debian system.
> So far I installed postgres and created a user and a database for galaxy.
> In the universe_wsgi.ini file I did the recommended changes and set this
> en
Tena Sakai wrote:
> Hi
>
> I am a developer for a group. I am having a problem with local installation
> of galaxy. The platform I am using is:
> $ uname -o
> GNU/Linux
>
> $ uname -i
> x86_64
>
> $ uname -v
> #1 SMP Tue Jul 22 18:01:05 EDT 2008
>
> $ uname -r
> 2.6.9-78.0.1.
Nate Coraor wrote:
> >
> > $ uname -v
> > #1 SMP Tue Jul 22 18:01:05 EDT 2008
> >
> > $ uname -r
> > 2.6.9-78.0.1.ELsmp
RHEL 4, I believe?
> > $ cd galaxy-dist
> > $ sh run.sh
> ><...lots of lines here...>
> &
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 gal
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=a799d38679e985db&show_deleted=False&cntrller=library&folder_id=0a248a1f62a0cc04&use_panels=False&id=dff4190d28
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
my question: Is there a way to run galaxy on ports other
> than 8080?
Yes, in the file universe_wsgi.ini in the root of the Galaxy directory,
one of the options near the top of the file is 'port ='. This can be
changed to whatever you prefer.
--nate
>
> Thank you!
>
> Re
0 51116 668 pipe_w S+ pts/9 0:00 grep
> 28721
>
> Any clue, why I can't get there by browser?
>
> Thank you.
>
> Regards,
>
> Tena Sakai
>
>
>
> On 2/17/11 12:57 PM, "Nate Coraor" wrote:
>
> > Tena Sakai wrote:
>
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
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:
>
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 galax
Ryan Golhar wrote:
> I'm setting up Galaxy to run on my cluster using drmaa. I can see
> jobs getting submitted to Torque however the jobs keep failing,
> because the tools are in the default system path.
>
> How do I tell galaxy to append a directory to the path used by jobs?
Hi Ryan,
Whatever
Ryan Golhar wrote:
>
> >Ryan Golhar wrote:
> >>I'm setting up Galaxy to run on my cluster using drmaa. I can see
> >>jobs getting submitted to Torque however the jobs keep failing,
> >>because the tools are in the default system path.
> >>
> >>How do I tell galaxy to append a directory to the pat
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,
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
Revival! (This thread was sitting "flagged" in my mailbox since
November)
Peter wrote:
> Hi all,
>
> I've since restarted with a clean clone of the repository, and see the
> same problems. See:
>
> http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-October/003625.html
> http://lists.bx.psu.edu/pi
Steve Taylor wrote:
> >
> >I think so. Just to double check is there a definitive way I can tell? In
> >./tools/data_source/upload.xml
> >
> >
> >
>
>
> So I got this to work by hacking basic.py.
>
> def visible( self ):
> self.tool.app.config.ftp_upload_dir = '/data/galaxy'
>
it should be something we can add to
the job template.
--nate
>
> Best,
>
> Florent
>
>
> On 16/02/11 05:58, Nate Coraor wrote:
> >Hi Florent, et. al.,
> >
> >I've moved the discussion over to galaxy-dev since it pertains to local
> >i
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. T
Peter wrote:
> On Mon, Feb 21, 2011 at 2:43 PM, Nate Coraor 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 li
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 dis
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
Zachariah K Zachariah wrote:
> Hello,
>
> I am having some trouble compiling SAMtools on a Solaris10 X86 p latform
> using gcc compiler version 3.4.6. Using the Makefile I get some link errors
> and have not been successful in creating the binary or the associated
> libraries. It seemed to me
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 load
hari krishna wrote:
> Hi,
>
> What is the difference between threadpool_workers and
> local_job_queue_workers*.*
Hi,
threadpool_workers is the number of threads which will be available to
serve web requests. This means the number of possible concurrent
browser connections, but this valu
ou have come across this
> error before.
>
> Many thanks for your time.
>
> Regards,
> Sonali
>
>
>
>
>
>
> -Original Message-
> From: Nate Coraor [mailto:n...@bx.psu.edu]
> Sent: Tuesday, February 15, 2011 10:30 PM
> To: Sonali A
window.
The easiest way for users to set and send in the full error report is to
set the 'smtp_server' and 'error_email_to' options in universe_wsgi.ini.
This will enable the "bug report" icon you see on our public server.
--nate
>
> Thanks and Regards
&
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 defa
are sending your staff members to Galaxy
> Community 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 wrot
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 attrib
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'
Christian Hundsrucker wrote:
> Hi all!
>
> I want to load a R-workspace within a galaxy module (.rdat-file,
> R-Project) and therefore built the galaxy-.rdat datatype (binary).
> .rdat-files are gzipped and are only recognized within R if they are
> still zipped.
> However, the corresponding .dat-
Ryan Golhar wrote:
> Hi all - I'm uploading datasets into my local instance by importing
> from the filesystem w/o copying into Galaxy.
>
> Importing of uncompressed files works properly. The files I'm
> importing are owned by user1 and a read-able by everyone, including
> the galaxy user. The g
Paul-Michael Agapow wrote:
> This is not a Galaxy problem per se, but a problem during Galaxy setup
> so maybe others will have an insight.
>
>
>
> So we're installing our own Galaxy for production / general use. I've
> been following the config and advanced config guides and installed
> Galaxy
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
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 th
number, a single file size, or total files size loaded by one user(account)?
Galaxy does not have any built-in limitations on file size/count.
--nate
>
>
> Please find the attached screenshoots for your reference.
>
> Looking forward to hearing from you.
>
> Bes
Yanji Xu wrote:
> Dear Sir/Madam,
>
> I installed galaxy in my local server, then I tried to upload a 4.7 Gb fastq
> file into galaxy, but failed. Below is the error message.
>
> OverflowError: signed integer is greater than maximum
>
> How could I upload large data files into galaxy and proce
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 h
Peter Cock wrote:
> On Mon, Mar 7, 2011 at 5:56 PM, Nate Coraor 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
> >>
Brad Chapman wrote:
>
> > We made a decision when we implemented libraries that we would provide
> > fine grained security at the dataset level. The trade-off, obviously,
> > is that it takes time to check every dataset. Another approach to
> > solve this would be to not provide as fine-grained se
SHAUN WEBB wrote:
>
> Further to my email below.
>
> I have a data library that contains many ~117Gb of NGS data,
> uploaded via file system path. This library was always slow to open
> (about 10s) but now takes several minutes or not at all.
>
> Thanks for any help on this. I am still experienc
Yanji Xu wrote:
> Dear Sir/Madam,
>
> Does Galaxy support parallel computing?
Yes, please see the information about using a cluster at:
http://usegalaxy.org/production
--nate
>
> Thanks,
> Yanji
> ___
> Please keep all replies on the
Ry4an Brase wrote:
> As use of our Galaxy installation is picking up, we're getting a lot of
> requests for greater fairness and transparency in the Galaxy job runner
> area.
>
> As I understand things the primary tool Galaxy gives us to affect
> processing order and wait times with our torque-bas
Peter Cock wrote:
> $ sh manage_db.sh upgrade
> Traceback (most recent call last):
> File "./scripts/manage_db.py", line 12, in
> from migrate.versioning.shell import main
> ImportError: No module named migrate.versioning.shell
This is a bug, but as a workaround try the following:
python
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 mach
Glen Beane wrote:
> >
> > I'd prefer to keep most of the scheduling in the DRM (Torque, SGE, etc.)
> > since that's what it's designed to do. That said, we want to make it as
> > easy as possible to do this, and Galaxy currently only sort of has the
> > ability to do it. By currently I mean that
Peter Cock wrote:
> On Tue, Mar 15, 2011 at 3:18 PM, Nate Coraor wrote:
> > Peter Cock wrote:
> >
> >> $ sh manage_db.sh upgrade
> >> Traceback (most recent call last):
> >> File "./scripts/manage_db.py", line 12, in
> >> f
James Lindsay wrote:
> Hi,
> I run galaxy on a large SMP university machine. The machine is used
> by some folks for command line work, and others via galaxy. I was
> wondering if anyone had integrated into galaxy a job manager that
> monitors CPU load averages, and only runs new jobs when cpu
> re
Nate Coraor wrote:
> James Lindsay wrote:
> > Hi,
> > I run galaxy on a large SMP university machine. The machine is used
> > by some folks for command line work, and others via galaxy. I was
> > wondering if anyone had integrated into galaxy a job manager that
> >
Bonci, Timothy Daniel wrote:
> I currently have a Python script that outputs an HTML with an embedded
> Applet. The Java is installed under /tools/blah and I have the archive=../../../tools/blah> which should appropriately step out of the
> dataset space where the HTML wants to execute, but it
Isabelle Phan wrote:
> Uploaded data from Biomart and the data is displayed correctly in the middle
> pane.
> I deleted all datasets in the history except the first one (a fastq file),
> and it now displays correctly too!
>
> I upload a fasta file: it does not display.
>
> Could this be a bug w
Peter Cock wrote:
>
> $ python -ES ./scripts/fetch_eggs.py
> Fetched http://eggs.g2.bx.psu.edu/Mako/Mako-0.2.5-py2.6.egg
> Fetched
> http://eggs.g2.bx.psu.edu/pysam/pysam-0.4.1_kanwei_ae2bd50d9945-py2.6-macosx-10.6-universal-ucs2.egg
> Fetched http://eggs.g2.bx.psu.edu/Babel/Babel-0.9.4-py2.6.egg
Peter Cock wrote:
> > Were there really no eggs, or did you remove your eggs directory prior
> > to running this fetch?
>
> I can't tell you if there were no eggs (I'm fairly sure there were
> some), but I hadn't removed any deliberately. Might that have
> happened via hg update clean?
I'm prett
Liisa Koski wrote:
> Hello,
> I have a local instance of galaxy and after successfully running an NGS
> analysis I am trying to save my BAM file to my local machine. When I click
> on the save icon my Galaxy instance crashes with the following error. This
> also happens when I try to save the SA
Louise-Amélie Schmitt wrote:
> Hello
>
> We managed to install Galaxy according to the unified method, with the
> runner and the web application running on separate machines sharing by
> NFS the same storage space where the Galaxy files are.
>
> The thing is, the data must be saved in another NFS
Ryan Golhar wrote:
> Hi all - I was about to update my local Galaxy installation, and
> went back to the wiki to refer to how to do this
> (https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy), and
> noticed a mistake.
>
> Step 1 says to use "hg clone https://bitbucket.org/galaxy/galaxy-dis
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
Assaf Gordon wrote:
> +1
>
> Nate Coraor wrote, On 03/31/2011 12:34 PM:
> > Ryan Golhar wrote:
> >>
> >> Nate - Is there a way to get the pbs job scripts to still get saved
> >> with debugging turned off?
> >
> > Not without modifying the ca
Yan Luo wrote:
> Dear Nate,
>
> I can't start my galaxy and got the following information, could you please
> let me know how we can fix it as soon as possible? We were running the
> system, it was down last night suddenly. Hope we can fix it today.
>
>
>
> File
> "/mnt/gluster-vol/home/kangt
p Galaxy in the
background with:
Start:
% sh run.sh --daemon
Stop:
% sh run.sh --stop-daemon
--nate
>
> Have a nice weekend!
>
> Best Wishes,
>
> Yan
>
> On Fri, Apr 1, 2011 at 10:37 AM, Nate Coraor wrote:
>
> > Yan Luo wrote:
> > > Dear Nate,
> &g
with the
'mysql' command line interface, it's up. If you are worried about
corruption, you can check the MySQL logs or use 'mysqlcheck'.
--nate
>
> Best Wishes,
>
> Yan
>
> On Fri, Apr 1, 2011 at 10:48 AM, Nate Coraor wrote:
>
> > Yan Luo
Ryan Golhar wrote:
> Hi all - Is it possible to define in a tool's XML file specific
> nodes in a cluster that the tool should run on?
>
> I have a few machines in my cluster is lots of RMA that I need for a
> specific tool. However there is no way to guarantee the tool will
> execute on one of t
Hi Sarah,
Does this occur with all histories? Does it change if you create a new
history?
--nate
Sarah Diehl wrote:
> Hi all,
>
> I encounter the same error that was already mentioned in this list
> (with the same email title). For me it also does only happen when
> debug is set to false. Howe
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 e
Assaf Gordon wrote:
> Until a better solution comes along, this tiny patch makes the temp files
> world-readable:
>
> http://cancan.cshl.edu/labmembers/gordon/files/apache_xsendfile_temp_files.patch
We avoid this by running our webserver as the Galaxy user. Obviously
not a solution for everyone
Ryan Golhar wrote:
> Speaking of which, the Wiki site hasn't been update to reflect that
> step 1 uses "hg clone https://bitbucket.org/galaxy/galaxy-dist/";
>
> and step 5 moves to galaxy-central. Is this supposed to be the case?
That was just a bit of incorrect output from 'hg incoming', but th
gt; Mike.
>
>
>
> On Thu, Apr 7, 2011 at 5:43 AM, Nate Coraor wrote:
>
> > Assaf Gordon wrote:
> > > Until a better solution comes along, this tiny patch makes the temp files
> > world-readable:
> > >
> > >
> > http://cancan.cshl.edu
Ryan Golhar wrote:
> Yeah, I installed back on Feb 18th, and just did a "hg incoming".
> hg reports nothing has changed. That doesn't sound correct.
Actually, February 18 was the date of our last stable release. The next
one is scheduled for tomorrow.
--nate
>
> On 4/7/11 12:13 PM, Assaf Gord
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 ^/galaxy/stati
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_qmas
Hi Johannes,
Johannes Eichner wrote:
> Dear Galaxy Team,
>
> I just updated my local instance of galaxy, and now I have a problem
> with the "DRMAA_python" egg, which makes it impossible to run jobs on
> our SGE cluster. I get the following error message after executing "run.sh":
...
> gcc -pth
Pieter Neerincx wrote:
> Hi Leandro,
>
> On Apr 27, 2011, at 6:08 PM, Leandro Hermida wrote:
>
> > Hi Pieter,
>
>
>
> > 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 u
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 loadin
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