Dear all,
I just started setting up a galaxy instance and I'm a bit stuck with
user account activation without e-mail. Is it possible to run Galaxy
without an SMTP server set?
For example, for the administrator user, I set:
admin_users =
in galaxy.ini . I'd also like to require login (i.e.,
Hi Dannon,
On Thu, Jul 30, 2015 at 4:28 AM, Dannon Baker wrote:
> Regarding activation, you mean you set user_activation_on = True, right?
> You can just leave 'user_activation_on = False', which is the default (and
> the value if left commented), which will disable any requirement of having a
>
Dear all,
We are in the middle of setting up a local Galaxy instance on CentOS,
but we have a problem with disk space. In particular, we do not have
a single large disk partition but, instead, many medium sized ext4
partitions. Thus, we were wondering if it would be possible for
Galaxy to use mu
Hi Bjoern,
Thank you for the prompt reply!
I didn't know what to look for, but now that you mention it, I can
search for "ObjectStore" in the configuration file... Looking at
object_store_conf.xml.sample, it looks like I can specify various
partitions and when data is stored. I presume when it
Dear all,
I'm still new to Galaxy but was wondering if someone could offer some advice.
On a local Galaxy instance, if I were the Galaxy administrator but do
not have sudo access on the machine itself, is this a problem? Or are
the two roles intricately linked so that the Galaxy administrator wi
Hi Peter,
On Tue, Sep 22, 2015 at 5:18 PM, Peter Cock wrote:
> Hi Ray,
>
> You will absolutely need command line access to the Galaxy
> server for some of the administration tasks - the web admin
> controls and web report tool only let you do some of the likely
> tasks.
>
> During the initial se
u for your advice!
Ray
On Wed, Sep 23, 2015 at 12:12 AM, Peter Cock wrote:
> On Tue, Sep 22, 2015 at 4:38 PM, Raymond Wan wrote:
>> Hi Peter,
>>
>>
>> On Tue, Sep 22, 2015 at 5:18 PM, Peter Cock
>> wrote:
>>> Hi Ray,
>>>
>>> You will ab
Hi all,
I was wondering if anyone has experience with setting up Galaxy with
SLURM. I'm not sure if this is the same for other DRMAAs, but what I
would like to do is use a server for both Galaxy and command-line job
execution. Thus, I would like both to add jobs on to the *same* queue
(i.e., par
Hi Mic,
On Wed, Dec 16, 2015 at 10:35 AM, Mic wrote:
> Where do I insert the following settings?
>
> RewriteEngine on
> RewriteRule ^/static/style/(.*)
> /home/galaxy/galaxy/static/june_2007_style/blue/$1 [L]
...
They should probably go in
/etc/apache2/sites-available/000-default.conf . If you
Dear all,
I'm a bit new at being a Galaxy administrator, so apologies for the
basic question.
I need to install some bowtie and bowtie2 indices. I have the indices
already but came across this page:
https://wiki.galaxyproject.org/Admin/DataPreparation
which says the steps mentioned on that pag
imes are very long. Since I have the
FASTA file already, it might be easier to upload one myself; but if
that's not something Data Managers can do, I guess I can just start
the download and set it aside...
Thank you!
Ray
On Thu, Feb 18, 2016 at 8:36 AM, Raymond Wan wrote:
> Dear all,
>
>> unrelated to Galaxy), download times are very long. Since I have the
>> FASTA file already, it might be easier to upload one myself; but if
>> that's not something Data Managers can do, I guess I can just start
>> the download and set it aside...
>>
>> Thank yo
fashioned' ;)
>
> we still solely rely on manually editing the '*loc' files. The main reason
> we do that: Most of our reference data is first prepared (by others) for
> people using it on the command line, and only in a second step we make it
> available via Gala
Hi Peter,
On Thu, Feb 18, 2016 at 4:13 PM, Peter van Heusden wrote:
> Hi Ray
>
> Data Managers are designed to co-exist with manually editing the .loc files.
> So don't worry, edit away.
Thank you for the clarification! That made me feel better and I
pressed ahead and just got it working.
Wh
Dear all,
I know Galaxy is independent of the underlying queuing system but is
it possible to display the status of the queue to users via the Galaxy
interface?
I understand that the jobs are submitted under the name of the owner
of the Galaxy process. And that there is a way to fix this [1], bu
jobs" page.
>
> This is probably the easiest way - though you need to consider, that all
> users can see each other jobs (i.e the executed command line) on that extra
> web site
>
>
> Regards, Hans-Rudolf
>
>
>
>
> On 04/15/2016 09:22 AM, Raymond Wan wrote
Dear all,
We are experiencing a crash of our Galaxy instance (latest git log is
early January 2016) and it seems unable to restart. The last entries
in paster.log says the following:
galaxy.web.framework.base DEBUG 2016-05-24 17:46:42,593 Enabling
'histories' API controller, class: HistoriesCon
Hi Peter,
On Tue, May 24, 2016 at 6:29 PM, Peter Cock wrote:
> In case you didn't know, Galaxy likes to keep all BAM files in
> coordinate sorted order with a BAI index (using samtools).
> Somehow this is failing on your system (perhaps a suitable
> version of samtools is not on the $PATH).
No
Hi Peter,
On Tue, May 24, 2016 at 6:29 PM, Peter Briggs
wrote:
> One of my colleagues encountered a similar-sounding error on our local test
> instance, where an unsorted BAM file seemed to crash the Galaxy handler
> processes and prevented them from restarting.
>
> In our case the default samto
t;
> $ cat local_env.sh
> # Prepend samtools 1.2
> export PATH=$HOME/apps/samtools/1.2/bin:$PATH
> ##
> #
>
> which is automatically picked up by 'run.sh' when Galaxy is started (I don't
> know how that plays if you're using a uwsgi/supervisor setup).
Dear all,
I'm trying to install a Galaxy tool (cummeRbund; the one from devteam)
and I'm getting the following error during installation:
-
Proxy Error
The proxy server received an invalid response from an upstream server.
The proxy server could not handle the request POST
/admin_toolshed/pr
is kind of problem in the Tool Shed?
Thank you for your help!
Ray
On Fri, Jun 3, 2016 at 1:08 AM, Raymond Wan wrote:
> Dear all,
>
> I'm trying to install a Galaxy tool (cummeRbund; the one from devteam)
> and I'm getting the following error during installation:
>
evelopers
> themselves, then reporting it on this mailing list should also
> reach the relevant people.)
>
> Peter
>
>
> On Tue, Jun 7, 2016 at 4:40 AM, Raymond Wan wrote:
>> Dear all,
>>
>> Sorry to bring this up again, but I've been so far unable to
Dear all,
I'm trying to run the JBrowse tool within Galaxy. The installation
was fine (I think), but when I run the tool, I get this error:
Fatal error: Exit code 1 () Traceback (most recent call last): File
"/d15/galaxy/shed_tools/toolshed.g2.bx.psu.edu/repos/iuc/jbrowse/d022577ff9cf/jbrowse/j
Hi Ryan,
On Sat, Jul 9, 2016 at 12:40 AM, Ryan G wrote:
> Hi Martin - I was actually thinking to let the tool itself tell Galaxy about
> the progress instead of Galaxy estimating that.
>
> If instance, if the tool know it has 5 stages, it can report back to Galaxy
> 20,40,60,80,and 100 % complet
Dear all,
I've been having some problems with some tool dependencies. With most
of them, after a few iterations of uninstall and install, the problem
seems to go away. (I'm not too sure about the reason as I didn't take
good notes while working out the problem to determine what I finally
did righ
Hi Anthony,
On Wed, Jul 27, 2016 at 11:16 PM, Tony Schreiner
wrote:
> I have galaxy server 15.10 running on Ubuntu 14.04, which has python 2.7.5.
>
> I was in the process of adding matplotlib from the toolchest. It has a
> dependency on package_python_2_7.
>
> Before proceeding, I'd like to unde
Dear all,
I'm not sure but I think I found a bug somewhere. However, I can't
tell where the problem is and, so, who to report it to.
This is what I see in paster.log:
-
galaxy.jobs.runners.drmaa DEBUG 2016-08-01 13:02:08,895 (897/193391)
state change: job finished normally
galaxy.jobs.outpu
t;
> Obviously you may want to fix the cause of the job failure, but it don't
> think that this is due to a bug in drmaa or Galaxy itself, probably just the
> cufflinks dependency you mentioned.
>
> Cheers,
> Nicola
>
>
> On 02/08/16 10:42, Raymond Wan wrote:
>>
&
Hi Eric,
On Wed, Aug 17, 2016 at 4:31 AM, Eric Rasche wrote:
> Hi Ray,
>
> Sorry I missed this mail.
No problem! Thanks for getting back to me!
> On 23. juni 2016 10:27, Raymond Wan wrote:
> I'm trying to run the JBrowse tool within Galaxy. The installation
> was f
Hi Jochen,
I presume you looked at this already:
https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
Those instructions work for Ubuntu as well. What do your Apache2
error logs says (in /var/log/apache2/)? And what have you tried in
your configuration files?
And are you trying to forward
Hi Jochen,
On Fri, Sep 2, 2016 at 8:32 PM, Jochen Bick wrote:
> yes exactly. So my problem is that I have no idea where to copy those
> settings. I have tutorial how it works on Centos but the file structure is
> different on Ubuntu.
Slightly different, but not too different. If it's Apache t
Hi Jochen,
On Sat, Sep 3, 2016 at 2:31 AM, Bick Jochen wrote:
> RewriteEngine on
> RewriteRule ^(.*) http://localhost:8080$1 [P]
...
> but it does not have any effect. Here the error.log but there is no error:
> [Fri Sep 02 15:28:21.677881 2016] [mpm_event:notice] [pid 6627:tid
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