Just to follow up on this thread -- we resolved this over IRC. It was a
proxy configuration issue with nginx's upload_config settings.
Correct settings are now on the wiki, but the previous rule for: location
_upload_done : set $dst /tool_runner/index; is was causing a redirect and
preventing
Hi Dannon,
so the very last line (set $dst /galaxy/tool_runner/index;) on the
wiki page https://wiki.galaxyproject.org/Admin/Config/nginxProxy is
still wrong?
Ciao,
Nicola
Il giorno ven, 10/10/2014 alle 08.50 -0400, Dannon Baker ha scritto:
Just to follow up on this thread -- we resolved this
D'oh. It's correct in the block right above that, but incorrect there.
I'll fix it now.
On Fri, Oct 10, 2014 at 9:44 AM, Nicola Soranzo sora...@crs4.it wrote:
Hi Dannon,
so the very last line (set $dst /galaxy/tool_runner/index;) on the
wiki page
(And thanks for the catch!)
On Fri, Oct 10, 2014 at 9:48 AM, Dannon Baker dannon.ba...@gmail.com
wrote:
D'oh. It's correct in the block right above that, but incorrect there.
I'll fix it now.
On Fri, Oct 10, 2014 at 9:44 AM, Nicola Soranzo sora...@crs4.it wrote:
Hi Dannon,
so the very
Hi Melissa,
It is possible to do things like this using dynamic_options and a code file,
which are somewhat deprecated, but still usable. An example that you might want
to look at could be the GenomeSpace Export tool
(tools/genomespace/genomespace_exporter.*), which queries the GenomeSpace API
Hi Damion,
Text fields are not currently able to be populated by dynamic_options, but in a
dynamic_options select list you could access the user’s username directly. If
you want the user to be able to override it, you could have a conditionally
used empty text box that your tool defaults to
Hi John,
The difference with an external settings-only file and the third option is
that the last one has settings and layout mixed up. Say we want to change the
order of two fields in a form, then with the macros approach I would need to
change N macro files for N different versions (each
Hi Dan,
I'd like to get the user's galaxy user name directly - but the code
file=... that drives my dynamic_options select list has no access to any
information in a galaxy's user session, right? (Ultimately I'm trying to get
the dynamic_options code to make galaxy api calls using the user's
Hi Damion,
In the genomespace exporter case, the call to
“dynamic_options=galaxy_code_get_genomespace_folders( genomespace_site =
'prod', trans=__trans__, value=__value__, input_dataset=input1,
base_url=base_url )”” is passing in trans, which it is using to determine user
and an attribute of
Anyone else having issues using cloudman version of galaxy?
No matter what set of AWS keys I use to try to start a new galaxy
cluster I always get the vague
Bad Request : Instance failure, but no specific error was detected.
Please check your AWS Console.
... error on the launch screen.
Hi Chris,
How are you trying to start these clusters?
And, the one you started successfully, how did you start it?
-Dannon
On Fri, Oct 10, 2014 at 1:24 PM, Chris Dagdigian d...@sonsorol.org wrote:
Anyone else having issues using cloudman version of galaxy?
No matter what set of AWS keys I
Just realized you said cloudlaunch in the subject there, so I'm assuming
that's what you used. For both working and non-working clusters? And this
is cloudlaunch on usegalaxy.org? I can check the logs for more detailed
launch failures, if so.
On Fri, Oct 10, 2014 at 1:27 PM, Dannon Baker
Appreciate the fast reply! I'm at a training session where I hope to
spin up 24 cloudman managed galaxy instances so each student can have a
1:1 ownership of their own cluster
I used this URL to fire up my test cluster:
https://usegalaxy.org/cloudlaunch
... but the test cluster is running out
The errors I'm seeing in the logs relate to virtualization required baked
into the AMI for the large memory instances. This is an error on our side
related to new instance types.
What I'd recommend to get off the ground immediately (with reasonable
memory on a node) would be to use the
Much appreciated - thanks again for the diagnosis and helping me confirm
that I was not fat-fingering anything on my end!
Currently I have a c3.4xlarge instance that booted directly from the AWS
console using the current AMI referenced on the cloudlaunch page. It's
waiting at the cloudman admin
Hi Team,
I am sorry to be a pest, but I am under-the-gun to get this resolved. I have
followed the instructions for installing GATK2 on my cloud VM. After doing
that I discovered that the version of java running on the VM was v1.6.x and
GATK2 required v1.7.0x. I removed version 6 and
Just a paranoia check ...
I manually started the cloudman galaxy AMI (ami-a7dbf6ce) and noticed
that it is configured and running a boinc client
Just wanted to check if this was legit and expected ...
Regards,
Chris
___
Please keep all
First guess is that perhaps the system is still defaulting to using java 1.6
and not 1.7. What happens if you run “java -version” as the Galaxy system user?
Perhaps try a reboot of the vm as well to make sure that the Galaxy app is
running with java 1.7.
Also, is this a custom vm? If it using
Hi Dan,
I had suspected that, but when I run java –version I get the following:
java version 1.7.0_65
OpenJDK Runtime Environment (IcedTea 2.5.1) (7u65-2.5.1-4ubuntu1~0.12.04.2)
OpenJDK 64-Bit Server VM (build 24.65-b04, mixed mode)
I have rebooted the VM and nothing has changed. The VM is
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