Are you using multiple web processes, and are you referring to the old admin
tool reloader or the toolshed reloading interface?
-Dannon
On Feb 5, 2013, at 9:13 PM, Anthonius deBoer wrote:
> Hi,
>
> I find that reloading a tool's configuration file does not really work.
> First, you have to cl
Hi,I find that reloading a tool's configuration file does not really work.First, you have to click the reload buttow twice to actually have it update the VERSION number (so it does read something)...But when I try to run my tool, the old bug is still there...I am using proxy server so something may
I am trying to define a colleagues association table that can be used to notify
people when there colleagues make changes. Think of it as a Facebook
"followers" type of thing.
The relationship is not necessary inverse. I may follow James Watson, he might
not (yet) follow me. ;-)
Anyhow, here
Dear Galaxy Project community,
I am working with a group of students at College of Charleston
of South Carolina. Being interested in bioinformatics and software
engineering, we chose to work on Galaxy for our open source class project.
We are subscribed to the appropriate mailing list,
Dear Galaxy Project community,
___
Please keep 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:
http://lists.bx.psu.edu/
Hey,In our local galaxy install using the latest release january, uploaded datasets are showing empty. But when you download it the contents are there, also if you click auto-detect in edit attributes it will remove the empty status and allow peeking and such. If you upload via ftp the dataset does
I partially answered my own questions by reading the Tool Dependencies wiki
page.
I installed velvet to my workstation.
When I open the shell to start galaxy, I modify $PATH to include the velvet
directory.
Now the error I get in Velvet suggests it found the program, but something
else is wrong
So I am setting up my local Galaxy on a workstation for my own use.
I have installed several programs from the Assembly Main Tool Shed.
None works.
Are these just the wrappers? Do I need to install, say, Velvet somewhere
outside of Galaxy?
How do I do this?
My errors:
6: velveth on data 2
error
On Feb 2, 2013, at 1:02 AM, Prasun Dutta wrote:
> Hi Nate,
>
> Thanks for the reply. I have already installed VM and downloading Ubuntu now.
> I had some other queries:
Hi Prasun,
It's best to keep replies on the list, to ensure access to a wide audience of
people who may be able to provide b
On Jan 30, 2013, at 11:34 AM, Daniel Patrick Sullivan wrote:
> Hi, Galaxy Developers,
>
> I have a couple of hopefully quick questions regarding PBS integration with
> Galaxy;
>
> I noticed (based on taking a look at the PBS log data) that Galaxy
> authenticates rather frequently to the pbs_mo
On Jan 29, 2013, at 3:59 PM, Guest, Simon wrote:
> We have set up our local Galaxy installation to submit jobs by default
> through HTCondor, using the drmaa tool runner. We override this on a
> tool-by-tool basis in universe_wsgi.ini, to specify certain tools we always
> want to run locally.
Probably nothing wrong with the script, but my hunch is that the original $PATH
setting you did for the galaxy user doesn't persist to this script's
environment because it uses a non-login shell. I'm definitely not a CentOS
expert, but there's probably another file used for settings like this i
Thank you Dannon for pointing me to the right direction. I have been using a
script suggested in one of this forum to start it "service galaxy start/stop".
I never thought that would be a source of issue since it is calling "run.sh"
script anyway. However, I just tried "sh run.sh" and I did no
Hakeem,
What's going on here is that the BAM metadata setting function doesn't use the
normal dependency methods and thus doesn't read 'env.sh' (which does look
correct), requiring 'samtools' to be available on the path of the galaxy user.
How are you executing galaxy itself? Are you positive
Have you restarted your galaxy instance after changing the setting? And, in
that drop-down, can you confirm that 'filesystem paths' is not an option?
Also, please keep conversations on-list so that others might be able to help
and/or benefit from the exchange.
-Dannon
On Feb 5, 2013, at 12:1
Hi,
I installed a local galaxy on Centos 6 and I followed the instructions on how
to install samtools/bwa/bowtie found here
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup.
I setup the correct env. for these programs correctly. Since I have no issues
with the bwa and bowtie so I assum
Only setting library permissions has been implemented. A new methods
would need to be added to this controller if you would like to read
library permission.
If you want to change the library permissions using the API, you can
post against that URL and include the following options in your
payload.
Hello,
I'm looking for a way to change library permissions using galaxy API.
When I look at the API documentation at the url
https://galaxy-dist.readthedocs.org/en/latest/_modules/galaxy/webapps/galaxy/api/permissions.html#PermissionsController
There is supposed to be a way to do that but when
Hi, Peter,
You are right, I thought there was already a datatype defined for PSSM, but
it turned out there isn't one yet. I attached a draft tool configuration
file for psiblast, it was based on the blastp configuration file, please
revise as you like.
The options that are specific to psiblast ar
Hi Dannon,
Thanks for the fast reply
On 5 February 2013 14:49, Dannon Baker wrote:
> Hi Eric,
The threading.Thread issue indicated below has been fixed (the changeset is
> already available in galaxy-dist) and isn't eclipse-centric.
>
Ok somehow I didn't get this update from
https://bitbucket
Hi Eric,
The threading.Thread issue indicated below has been fixed (the changeset is
already available in galaxy-dist) and isn't eclipse-centric.
>From eclipse, how are you launching galaxy?
Personally for debugging I've found it easier to use the debugging middleware
for anything that happens
On Mon, Feb 4, 2013 at 7:32 PM, Peter Cock wrote:
>
>
> On Monday, February 4, 2013, Luobin Yang wrote:
>>
>> Hi, Peter,
>>
>> Thanks for pointing them out!
>>
>> The phi-blast and psi-blast actually share the same binary, both use the
>> psiblast program in the NCBI BLAST+ tools. When the option
Hi All,
I am Running my local galaxy instance in Eclipse - pydev to make debugging
somewhat easier, but now I run into loads of Code errors. It seems that
pydev doesn't understand the Bunch() Class frequently used in Galaxy.
But also code errors that maybe could be fixed. such as:
lib/galaxy/job
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