I think that the best approach for this is an additional ToolDependency status
as John proposed a while back as this approach allows for the flexibility
needed to support just about anything users may want to do. I haven't had a
chance to look at this yet, and I'm currently working on a couple
Hi all,
I've just updated our main Galaxy to release_2013.11.04 but
also see the following problem on galaxy-central, and on
https://usegalaxy.org/ as well.
(1) Go to any history with deleted files
(2) Cog icon, tick Include Deleted datasets
(3) Look at a deleted dataset in your history column,
Hey Daniel,
Thanks so much for the details problem report, it was very helpful.
Reviewing the code there appears to be a bug in the PBS job runner -
in some cases pbs_job_state.stop_job is never set but is attempted to
be read. I don't have torque so I don't have a great test setup for
this
This seems to happen often e.g.
http://wiki.galaxyproject.org/DevNewsBriefs/2012_10_23#Compute_Tool_Security_Fix
a) are there general guidelines in the wiki on how to avoid these problems when
creating tools?
b) is there a way to check automatically if all input fields are correctly
escaped in
Hello, Robert
I'm having difficulty reproducing this with a fresh install of
galaxy_central:default:11226:c67b9518c1e0.
Is this an intermittent error or does it happen reliably each time with the
steps above? Is it still the same javascript error you mentioned above?
I'll investigate further.
Hello, Peter.
Thanks for the report. There was an error in the javascript error handling
of purge_async which is now fixed in stable:11227:151b7d3b2f1b.
In the instances you mention, you should now see an error message in the
history 'Unable to purge this dataset': This is because of two
Hi Greg,
I'm right now in implementing a setup_perl_environment and stumbled
about a tricky problem (that is not only related to perl but also for
ruby, python and R).
The Problem:
Lets assume a perl package (A) requires a xml parser written in C/C++
(Z).
(Z) is a dependency that I can import
Hi Ido,
Thanks for the feedback. Replies below.
On Nov 5, 2013, at 9:54 AM, Ido Tamir wrote:
This seems to happen often e.g.
http://wiki.galaxyproject.org/DevNewsBriefs/2012_10_23#Compute_Tool_Security_Fix
I'm not sure I'd agree that it's often - we've had 4 or 5 vulnerabilities over
the
On Nov 5, 2013, at 6:28 PM, Nate Coraor n...@bx.psu.edu wrote:
Hi Ido,
Thanks for the feedback. Replies below.
On Nov 5, 2013, at 9:54 AM, Ido Tamir wrote:
This seems to happen often e.g.
http://wiki.galaxyproject.org/DevNewsBriefs/2012_10_23#Compute_Tool_Security_Fix
I'm not
Hi Dev Team,
I have run into an egg distribution issue. I had performed an upgrade late
last month and am experiencing issues fetching eggs. I am getting the
following error message:
galaxy@jaxgalaxydev01:/hpcdata/galaxy-dev/galaxy-setup/galaxy-dist python
./scripts/fetch_eggs.py
Fetched
Hello Bjoern,
On Nov 5, 2013, at 12:13 PM, Bjoern Gruening bjoern.gruen...@gmail.com wrote:
Hi Greg,
I'm right now in implementing a setup_perl_environment and stumbled about a
tricky problem (that is not only related to perl but also for ruby, python
and R).
The Problem:
Lets
Hi Greg,
Hello Bjoern,
On Nov 5, 2013, at 12:13 PM, Bjoern Gruening bjoern.gruen...@gmail.com
wrote:
Hi Greg,
I'm right now in implementing a setup_perl_environment and stumbled about a
tricky problem (that is not only related to perl but also for ruby, python
and R).
Thanks Björn,
We'll have to digest this a bit and we'll get back to you.
Greg Von Kuster
On Nov 5, 2013, at 4:35 PM, Björn Grüning
bjoern.gruen...@pharmazie.uni-freiburg.de wrote:
Hi Greg,
Hello Bjoern,
On Nov 5, 2013, at 12:13 PM, Bjoern Gruening bjoern.gruen...@gmail.com
wrote:
Perl complicates things, TPP complicates things greatly.
Bjoern, can I ask you if this hypothetical exhibits the same problem
and can be used to reason about these things more easily and drive a
test implementation.
So right now, Galaxy has setup_virtualenv which will build and install
Python
Dear all,
I would like to set up a local Galaxy instance behind an Apache server with our
local CAS for authentication.
It would be great if you could give me a hint for the httpd.conf. I have the
problem that after authenticating against CAS in the browser, I get following
error message and
Hi,
I updated my galaxy distribution with
hg pull -u
Then tried to re-run galaxy and got an error:
$ ./run.sh
Traceback (most recent call last):
File ./scripts/paster.py, line 33, in module
serve.run()
File /home/microbeco/galaxy-dist/lib/galaxy/util/pastescript/serve.py, line
1049,
Hi Robert,
We are currently working on improving data libraries including the speed
enhancements. In the meantime one of our users also reported that he is
using for the dataset folders multiple libraries - each having less
folder-depth which for him improves performance significantly. Maybe it
On Tue, Nov 5, 2013 at 11:53 AM, Daniel Patrick Sullivan
dansulli...@gmail.com wrote:
Hi, John,
Thank you for taking the time to help me look into this issue. I have
applied the patch you provided and confirmed that it appears to help
remediate the problem (when a walltime is exceeded
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