Hi,
I just wanted to jump in and point out real quick:
>> Did you restart pulsar after rolling out the new config ?
>
> to which you've answered that you re-ran the playbook, but that's not a
> sufficient answer.
> RUNNING HANDLER [galaxyproject.pulsar : default restart pulsar handler]
>
We use Groovy (actually our own Groovy DSL interpreter) extensively so it looks
like Groovy is not on the PATH that Galaxy is using. Can you log in to the
Docker instance and run Groovy scripts? What does Galaxy think its $PATH is?
Keith
> On Dec 26, 2016, at 3:23 AM, Anshul Tak wrote:
>
>
Jochen,
Two quick questions for you:
You say you can see the Apache instance from other machines on the network. I
assume you are accessing your machine via its local IP address (something like
192.168.1.x); what happens when you try to access Galaxy via
http://192.168.1.x:8080?
I see you are
, or maybe wheel installation, I can't think of anything
> that would have triggered anything like this on the Galaxy side.
>
> -Dannon
>
> On Wed, Jul 13, 2016 at 5:31 PM Suderman Keith <mailto:suder...@cs.vassar.edu>> wrote:
> We are in the process of instal
We are in the process of installing a Galaxy instance to Amazon EC2 and this
morning I received an email from ec2-ab...@amazon.com saying that our EC2
instance has been flooding 45.64.64.40 with data in what looks like a DOS
attack. A whois shows that the IP belongs to Incapsula, which appears t
> On Jun 29, 2016, at 7:02 AM, Philipp Rathert
> wrote:
>
> Hi Ido,
>
> I get no error message, but the command does not change anything. Rights are
> still assigned to host user and not to postgresql.
>
> Could it be that, since galaxy and other program were running in a docker
> container
g and doesn't really match user
> expectations. I'll see what I can do about that and possibly make it an alias
> to the above API when/if that makes it to a release. In any event, again,
> I'll double check that it's at least doing that.
>
> I'll also
f the bio/blend
> libraries.
>
> Failing the above, is there some way to get the history ID from the UI?
>
> You can click the information button ('i' with a circle around it) for any
> dataset in a history. The encoded history API id will be listed under:
> history a
I have been looking at the JavaDoc for Blend4J [1] and the REST API [2], but I
don’t see any way to obtain the “current” history as selected by the user in
the Galaxy UI. I see `/api/histories/most_recently_used`, but it seems that
simply selecting a history as the current history in the UI doe
t;
>>> On May 9, 2016, at 2:19 AM, Björn Grüning
>>> wrote:
>>>
>>> Hi Keith,
>>>
>>> please try this:
>>>
>>> c.MappingKernelManager.default_kernel_name =
>>> 'your_kerne_name...maybe_groovy'
>>>
>&g
t;
> completely untested. I would be happy to include the groovy stuff in the
> main image :)
>
> Thanks,
> Bjoern
>
>
> Am 09.05.2016 um 01:20 schrieb Suderman Keith:
>> How do I make my custom kernel the default when starting a Jupyter
>> interactive en
How do I make my custom kernel the default when starting a Jupyter interactive
environment?
I have written a native Jupyter kernel for Groovy, that is, a Jupyter kernel
written in Groovy that listens to, and responds on, the appropriate ZMQ
sockets. I have also extended the bgruening/docker-ju
I’ve heard back from one person. Would it help if I said that the Lappsgrid
project is buying lunch? :)
> On Apr 21, 2016, at 11:41 PM, Suderman Keith wrote:
>
> Sorry for spamming the list, but I thought this would be the easiest/quickest
> way to reach out to any interested peo
Sorry for spamming the list, but I thought this would be the easiest/quickest
way to reach out to any interested people in State College.
I had to make a short-notice trip to meet with colleagues in Pittsburgh and I
will be driving home to NY Saturday. Since I am driving right by State College
all replies on the list by using "reply all" in your
>>>> mail client. To manage your subscriptions to this and other
>>>> Galaxy lists, please use the interface at:
>>>> https://lists.galaxyproject.org/ <https://lists.galaxyproject.org/>
>>>>
>>>> To search Galax
Hi Björn,
> Yes it is, but you need the :dev version,
DOH, I should have known…
> Can you explain what you delete? I do really support this idea as we are
> also developing cheminformatics or imaging flavours.
Currently I think I have just removed the datatypes. I haven’t removed
anything els
ance with the default tools.
>
> Yes it is, but you need the :dev version, aka:
>
> docker run -i -t -p 8080:80 bgruening/galaxy-stable:dev
>
> (hope it works, I'm currently not on my PC)
>
>> Also, does this really give me a “bare” Galaxy instance, or just a
>
.md#extending-the-docker-image
>
> Hope this helps, I will merge the PR over the weekend hopefully.
>
> Cheers,
> Bjoern
>
> Am 31.03.2016 um 22:17 schrieb Suderman Keith:
>> Dear Galaxy Team,
>>
>> Two questions.
>>
>> 1) Is there a bare-bones
client/galaxy/’)
> that we modify outside of Galaxy and use a modified ‘GruntFile.js’
> (with different ‘dest’ targets) to make grunt(1) propagate our changes
> into the Galaxy tree.
>
> maybe some of these techniques could work for you too? oe
>
>
> On Thu, Mar 31, 2016
Dear Galaxy Team,
Two questions.
1) Is there a bare-bones version of Galaxy available somewhere? That is,
Galaxy with no tools pre-installed? We are creating Ansible play books for
configuring Docker/Galaxy instances with our NLP tools installed. Currently we
are using a fork of the Galaxy
Hi Mic,
I based my startup script on the ones found here:
1.
https://wiki.galaxyproject.org/Events/GCC2012/TrainingDay/WS5?highlight=%28init.d%29
2. http://simison.com/brian/GalaxyAdmin_notes.html
HTH,
Keith
> On Dec 17, 2015, at 5:54 PM, Mic wrote:
>
> Hello,
> Where could I find INIT scrip
axy.pid is owned by root:root. I have attached my /etc/init.d/galaxy script. This is from a Ubuntu 12.04 system.-WillOn Wed, Nov 4, 2015 at 8:13 AM, Suderman Keith <suder...@cs.vassar.edu> wrote:Hi Will,I tried that and it didn’t work for me. Are you using start-stop-daemon to launch python?
adding the sourcing of
> .venv/bin/activate to the etc/init.d/galaxy script. Then none of the
> pre-existing pid code needs to be changed.
>
> -Will
>
>
> On Tue, Nov 3, 2015 at 8:55 AM, Suderman Keith <mailto:suder...@cs.vassar.edu>> wrote:
> The solution wa
I am not very good with Apache rewrite rules, but I think there is a problem
with (at least) the first rule. I see in the Apache documentation [1] that the
following “doesn’t make sense, not supported":
^/somepath(.*) http://thishost/otherpath$1 [P]
The [P] flag is for forwarding to a proxy, b
Very odd that you were getting “Address is use” errors then.. What have you
set the port to in your galaxy.ini file?
The missing index.html/index.php won’t make a difference to Galaxy, but it
might prevent Apache from starting up. I would put a simple index.html file,
say:
You should not see
Do you have another service running on 8081? I see the server is complaining
about that address already being in use. Also, do you have an index.html or
welcome.html in /var/www/html?
Cheers,
Keith
> On Nov 3, 2015, at 11:39 AM, Makis Ladoukakis wrote:
>
> Hello,
>
> Unfortunately I cannot
The solution was rather simple, once I figured it out.
The /etc/init.d/galaxy script was invoking scripts/paster.py script directly so
.venv/bin/activate was not being sourced. The solution was to modify
/etc/init.d/galaxy to call a startup script that sourced .venv/bin/activate
before startin
Hi Edgar,
I vote for a permission problem. I had to recently debug a volume/file
permission problem and the symptoms are identical: Galaxy claims it can't find
a file that actually does exist. Given that you said /home/galaxy is an NFS
mount I strongly suspect something there has changed. U
I'm going to trim the replies a bit so my comments are easier to find.
> Am 12.09.2015 um 00:09 schrieb Martin Čech:
>> In this case the naming kinda makes sense to me (lapps_stanford_2_0_0 and
>> lapps_stanford_2_1_0 that is). However could the remote Standford API
>> version be a parameter of t
Hi Martin,
On Sep 11, 2015, at 12:44 PM, Martin Čech wrote:
> Hi Keith,
>
> how is the NLP category working for you? Do you want it on Main Tool Shed?
The NLP category is working great. I am still in the early testing phase and
likely won't need anything in Main for some time yet, but Steve
Hi John,
I will try what we have against master. I just went through my old emails and
it looks like the developer branch was recommended in response to a UI issue I
experienced with large dataset collections and not the collections themselves.
For reference, the UI issue occurred when I inad
31 matches
Mail list logo
