Hi,
in order to restrict the access of a tool to logged users
I'm trying to use Cheetah for editing the xml config file.
I was wondering if a solution like the one below should work.
Although no errors are reported while loading the tool
it does not perform the check on the email address and
Hi Nate,
On Jan 3, 2012, at 10:15 PM, Nate Coraor wrote:
That said, if you have a lot interim steps that produce large data that then
get merged via some process back to final outputs, it absolutely makes sense to
use local disk for those steps (assuming local disk is large enough - another
Does this functionality exist? If so, how do we get it working?
Sorry to bump!
On 1/3/12 8:50 AM, Matt Vincent matt.vinc...@jax.org wrote:
ost recent version of Galaxy.
___
Please keep all replies on the list by using reply all
in your
On Wed, Jan 4, 2012 at 5:24 AM, Timothy Wu 2hug...@gmail.com wrote:
Hi,
I'm executing a R script via Python's os.system() (using Rscript executable
which allow executing R script in the command line). This script makes use
of library that will attempt to load up Tcl/Tk interface. Though I
Hi Matt,
The asynchronous protocol should be working fine.
Can you confirm that your flow is similar to:
- User starts at Galaxy, gets sent to external resource with 'GALAXY_URL'
parameter.
- User browses external site and selects options, sends data to Galaxy by using
the GALAXY_URL
Thon,
This is a problem with the default client_max_body_size option in nginx being
set far too small in the nginx.conf on the cloud AMI. It'll be fixed with our
next AMI update, but you could also SSH in to your instance, edit the
nginx.conf to change the client_max_body_size to something
Hello,
1. How to define a character used at the beginning of a comment for ourput
file. i.e. if # is used at the start of the comment Galaxy recognises
this, but what if I want to use some other character.
is it possible to define this inside outputs?
outputs
data name=output
On Jan 3, 2012, at 8:35 PM, Huayan Gao wrote:
Thanks Nate!
I also want to do a mirror site of Galaxy Server in asia, but found the
instruction is not so clear/detailed. Do we have a detailed one?
Hi Huayan,
Please keep replies on the mailing list for the benefit and collaboration of
the
On Jan 4, 2012, at 4:40 AM, Cai Shaojiang wrote:
Thanks, Nate,
I now switched to MySQL, and the problem disappeared. Thanks.
The manual highly recommend postgresql, is there any critical point to
use it, instead of mysql? I am just more familiar with mysql. Thanks.
PostgreSQL support
On Jan 4, 2012, at 6:03 AM, Cittaro Davide wrote:
Hi Nate,
On Jan 3, 2012, at 10:15 PM, Nate Coraor wrote:
That said, if you have a lot interim steps that produce large data that then
get merged via some process back to final outputs, it absolutely makes sense
to use local disk for
I'm at the final stage of deploying our Galaxy instance. I'm implementing
the proxy server and load balancing with 1 job runner, and 5 web runners
using Apache. I'm following the guide on:
http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scaling
All the Galaxy
Usha:
Galaxy is essentially a wrapper around other command line tools.
So, while you could probably extract some of its pieces to run on the command
line, I don't know why you would want to.
brad
--
Brad Langhorst
New England Biolabs
langho...@neb.com
From: Usha Reddy
Hi,
While trying to import some fastq files to a data library, using
Upload directory of files and Link to files without copying into
Galaxy, I end with empty datasets.
My data files are accessed through NFS and I'm using the recommended
option -noac:
10.2.90.89:/projects on /local/projects type
On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad langho...@neb.com wrote:
Usha:
Galaxy is essentially a wrapper around other command line tools.
So, while you could probably extract some of its pieces to run on the
command line, I don't know why you would want to.
I would argue it would
On Wed, Jan 4, 2012 at 2:25 PM, Ryan ngsbioinformat...@gmail.com wrote:
On Wed, Jan 4, 2012 at 12:04 PM, Langhorst, Brad langho...@neb.com wrote:
Usha:
Galaxy is essentially a wrapper around other command line tools.
So, while you could probably extract some of its pieces to run on the
Ryan:
I didn't understand Usha's question the same way you did. I agree that it's
useful to run workflows in a more automated way.
I have not run workflows using the Galaxy API yet, but I did see some
documentation on it and plan to try it soon.
http://wiki.g2.bx.psu.edu/Learn/API/Examples
I have a cluster (cluster A) set up with Galaxy. Our sequencing data gets
mapped to hg19, then the resulting BAM files are placed on a SAN connected
to a different cluster (cluster B) that cluster A does not have NFS access
to. We cannot install an FTP server on cluster B either. The only way
On Tue, Jan 3, 2012 at 11:36 AM, Nate Coraor n...@bx.psu.edu wrote:
On Dec 20, 2011, at 1:09 PM, Bicak, Mesude wrote:
Dear Galaxy Developers,
We work in Professor Dawn Field's group (Molecular Evolution and
Bioinformatics Research Group) at the NERC Environmental Bioinformatics
Centre
On Jan 4, 2012, at 2:34 PM, Langhorst, Brad wrote:
Ryan:
I didn't understand Usha's question the same way you did. I agree that it's
useful to run workflows in a more automated way.
I have not run workflows using the Galaxy API yet, but I did see some
documentation on it and plan to
I'm adding Data Libraries to my local galaxy instance. I'm doing this by
importing directories that contain bam and bai files. I see the bam/bai
files get added on the admin page and the Message is This job is running.
qstat shows the job run and complete. I checked my runner0.log and it
On Wed, Jan 4, 2012 at 5:17 PM, Ryan Golhar ngsbioinformat...@gmail.comwrote:
I'm adding Data Libraries to my local galaxy instance. I'm doing this by
importing directories that contain bam and bai files. I see the bam/bai
files get added on the admin page and the Message is This job is
On Wed, Jan 4, 2012 at 12:59 PM, Carlos Borroto
carlos.borr...@gmail.com wrote:
Hi,
While trying to import some fastq files to a data library, using
Upload directory of files and Link to files without copying into
Galaxy, I end with empty datasets.
My data files are accessed through NFS and
On Wed, Jan 4, 2012 at 5:17 PM, Ryan Golhar
ngsbioinformat...@gmail.comwrote:
I'm adding Data Libraries to my local galaxy instance. I'm doing this by
importing directories that contain bam and bai files. I see the bam/bai
files get added on the admin page and the Message is This job is
Hi guys,
I am trying to setup a new galaxy for my institute. The galaxy itself runs
fine in our private network.
Now I am trying to configure the proxy so that it can be accessed publicly.
The official guide here
http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy
It seems to assume both
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