Thanks Greg.
1. Non-admin users with add permissions on a library are offered
the option to upload from file systems path. Should this be
restricted to admin users only?
Yes, this should be restricted to admin users only as access to the
file system for all users could result in undesir
Hi Nate,
We went through the mom_logs. We could see the jobs which were completed
successfully in Galaxy. However, the job/ tool run which failed were not seen.
These failed jobs were never submitted to PBS queue to be logged in the
mom_logs.
On another note, is the error, "pbs_submit failed, P
On further digging, we found that the script is failing in the following part
of $GALAXY_HOME/lib/galaxy/jobs/runners/pbs.py:
# submit
galaxy_job_id = job_wrapper.job_id
log.debug("(%s) submitting file %s" % ( galaxy_job_id, job_file ) )
log.debug("(%s) command is:
With the latest change set, non-admin users are not able to import files from
file system paths.
On Feb 15, 2011, at 5:35 AM, SHAUN WEBB wrote:
>
> Thanks Greg.
>
>>> 1. Non-admin users with add permissions on a library are offered the option
>>> to upload from file systems path. Should this
Yan Luo wrote:
> Dear Nate,
>
> Yes, you are right, for some reason, we couldn't cd to the folder. It is
> fixed and I restart the Galaxy. The only thing is that it needs about 10
> minutes to start. I remembered it is a little fast last week. Is there any
> problem? Anyway, Galaxy works.
Assumin
Sonali Amonkar wrote:
> On further digging, we found that the script is failing in the following part
> of $GALAXY_HOME/lib/galaxy/jobs/runners/pbs.py:
>
> # submit
> galaxy_job_id = job_wrapper.job_id
> log.debug("(%s) submitting file %s" % ( galaxy_job_id, job_file ) )
>
Hi Florent, et. al.,
I've moved the discussion over to galaxy-dev since it pertains to local
instances.
Florent Angly wrote:
>
> Indeed, this workaround works! Thank you.
> I added these lines to the beginning of my run.sh:
> PATH="/opt/local/bin:/opt/local/sbin:$PATH"
> export $PATH
>
When I try to load the megablast_wrapper tool, I get errors in the output:
AssertionError: Data table named 'blastdb' is required by tool but not
configured
I am totally confused how blastdb.loc should be configured. Is it one tab,
two, three?
David Hoover
Helix Systems Staff
http://helix.n
David,
this is what we have in blastdb.loc (nucleotide) or blastdb_p.loc (prot)a
snippettab delimited
caption can contain spaces so I increased the tab for display only
#This is a sample file distributed with Galaxy that is used to define a
#list of nucleotide BLAST databases, using three
I understand that it is best to flow with the logic of the underlying OS
and not too make too many platform-dependent assumptions about what
files should be read.
Perhaps, it seems like the best way to go would be to have a setting in
universe_wsgi.ini to specify a file to read additional envi
Hi - I'm running CentOS 5.5. My version of python is:
[root@genomes ~]# which python
/usr/bin/python
[root@genomes ~]# python -V
Python 2.4.3
I just downloaded galaxy to run a local instance using:
hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist
and then tried to run it using 'sh run.sh'
When I try to run 'python scripts/scramble.py', I get an error:
Traceback (most recent call last):
File "scramble.py", line 29, in ?
execfile( "setup.py", globals(), locals() )
File "setup.py", line 22, in ?
main_module = __import__(main_module_name, fromlist=['version'])
TypeError: _
Hi Ryan,
I think you might want to upgrade your Python version. I was facing this issue
and Python 2.6.6 version fixed it.
Regards,
Sonali
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
[mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Ryan Golhar
Sent: Wednesday,
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