So would the current correct method for setting up multi-threaded jobs on a
cluster be to specify custom runners in the [galaxy:tool_runners] section of
the universe config file for EVERY tool that uses a multiple threads
(assuming the default is set to one)?
For example, for the bowtie program
I would also like to voice my support for this feature. I wrote a wrapper
for bowtie that converts the SAM output to BAM after bowtie is finished just
to avoid the hassle of letting galaxy know that the SAM file existed
(didn't want to run Tophat).
After thinking about how I would go about
8cf8d25557b2
Hope this helps somebody.
Andrew Warren
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. There is a
loop there for slug creation and the following check OUTSIDE the loop:
if slug_set:
trans.sa_session.flush()
Should that be in the loop? Otherwise its just flushing the session if the
last workflow gets a slug created.
-Andrew Warren
with
our galaxy setup? I think we recently pulled updates for some major
tool_shed release but I haven't been able to determine if any of the
tools listed above were affected by that.
Wish I were in Český Krumlov asking this question. Missed the
registration deadline...doh.
Thanks,
Andrew Warren
the
registration deadline...doh.
Thanks,
Andrew Warren
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-V
-cwd
works for me.
On Wed, Jan 25, 2012 at 12:12 PM, Andrew Warren anwar...@vbi.vt.edu wrote:
Thanks for the replies. One extra element I failed to properly describe is
that we are running on a cluster with a similar setup to CloudMan. This
means we have a galaxyTools/tools
without using
all of them.
Cheers,
Andrew Warren
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, Peter Cock p.j.a.c...@googlemail.comwrote:
On Fri, Feb 10, 2012 at 4:18 PM, Jeremy Goecks jeremy.goe...@emory.edu
wrote:
On Thu, Feb 9, 2012 at 11:27 PM, Andrew Warren anwar...@vbi.vt.edu
wrote:
Hello,
I was recently adjusting advanced parameters when running Tophat in
Galaxy
and noticed
Hello,
In the file lib/galaxy/tools/actions/__init__.py for the execute function
of the DefaultToolAction class line 198 has the following code:
if trans.user and ( 'dbkeys' in trans.user.preferences ) and ( input_dbkey
in trans.user.preferences[ 'dbkeys' ] ):
In this case
.
Is the best way to deal with this just to create these files (even
though I am not using them)? Are these files being read every time a
web transaction goes down due to the property in
lib/galaxy/web/framework/__init__.py ?
@property
def ucsc_builds( self ):
Thanks,
Andrew Warren
?
Thanks for any help,
Andrew Warren
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To search
Hello all,
We are in the process of switching from SGE to SLURM for our galaxy setup.
We are currently experiencing a problem where jobs that are completely
successful (no text in their stderr file and the proper exit code) are
being hidden after the job completes. Any job that fails or has some
the corresponding dataset via the history API or in the
database and determine if they indeed are having visible set to False
- this I guess is what should cause a dataset to become hidden?
-John
On Fri, Nov 8, 2013 at 11:40 AM, Andrew Warren anwar...@vbi.vt.edu
wrote:
Hello all,
We
Hi all,
I was wondering if there were any existing implementations of, or any plans
for, a drill down selection component that supports thousands of items? For
example a taxonomy based drill down.
Thanks,
Andrew
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