Had some idea but they were all dead ends. How are you sourcing the
modules - in Galaxy's environment, using an environment file, using
Galaxy dependencies (env.sh files) or using Galaxy's modules support?
Do you have an example of such a module that sets LD_LIBRARY_PATH?
One thing to check is the
I have created a Trello card to track this request here
https://trello.com/c/qCtBBB8n.
Any chance you can share the tool with me? I understand that this
instinct is too simplistic - but it seems to me like the option to
repeatedly run a tool over many datasets should not be the concern of
the tool
Hello Galaxy Devs,
I was using data collections (for the first time) for a new workflow of ours and I
ran into this problem. There was no complaint by the workflow-editor and I could
start the workflow but then happened.
If you need more information about the workflow or otherwise let me know.
Hey,
Really intensive database operations including datasest collections
but other things too like multi-running tools or workflows over many
individual datasets for instance - can very easily overwhelm the
default sqlite database. This is frustrating and shouldn't happen -
but it does unfortuna
Enis, John and all;
I spotted ansible-cloudman on GitHub today which reminded me I've been
meaning to write about the approach we setup late last year to run bcbio
on AWS. It uses elasticluster (https://github.com/gc3-uzh-ch/elasticluster)
which has the advantage of being all Ansible scripts and b
Thanks for the pointer, this is great stuff and I had not seen it before.
I’ve wanted to do something similar for a while now, and it’s becoming even
more important as we loop in GCE. I’ll definitely read through and play with
this and see what we might be able to use, contribute back to, an
I'm still trying to debug this.
How do I change the working directory? I can't seem to find out how all
those directory mounts get passed to docker - the catDocker.xml appears to
generate a 'cat' command that I assume ends up in
()/job_working_directory/000/12/container.sh
but I can't find where t
Can you send me a screenshot of the Tool form right before you hit
submit. It is odd that two commands are executed barely differing at
all. There were some recent UI changes and I want to make sure that
you are passing two inputs once and not submitting one input twice in
the newly named "batch mo
Hello,
I am trying to setup a local production Galaxy server for our
department. Our Galaxy server environment is as follows:
- Ubuntu 14.04 64-bit
- 94 GB Memory
- Intel Xeon
- Python virtual environment
- Nginx
- PostgreSQL
- ProFTPd
Today I tried starting the Galaxy server for the first time.
See attached for screenshot!
Thanks for the links.
On Mon, Jan 26, 2015 at 11:37 AM, John Chilton wrote:
> Can you send me a screenshot of the Tool form right before you hit
> submit. It is odd that two commands are executed barely differing at
> all. There were some recent UI changes and I w
Howdy devs,
I put together a library recently, and since it seems to be functional I
thought I'd share with the rest of -dev in case it's of interest to anyone.
If anyone has feedback, bugs/issues, or PRs, I'd be happy to receive them!
https://github.com/erasche/gxargparse
So, what is it?
gxargp
Hi Nicholas,
Sorry for the somewhat misleading text in the documentation. The part about
"no extra modules or recompiling" refers to nginx itself - uWSGI protocol
support is built in to the core functionality of nginx. This does not mean
that uWSGI itself is installed. Installing uWSGI is addresse
Our sysadmin just notified me docker was taking up large amounts of space
in
/var/lib/docker/devicemapper/devicemapper/data
and
/var/lib/docker/devicemapper/devicemapper/metadata
I noticed the following DEBUG message in paster.log:
galaxy.jobs.runners.local DEBUG 2015-01-23 13:30:19,503 (12) exec
13 matches
Mail list logo
