lenta...@jimmy.harvard.edu wrote:
Hi,
I noticed on that on the manage users page, even after deleting and
purging users (by clicking on the delete and purge buttons on that page),
their account still sticks around in the db. How does one remove these
accounts permanently? Is there a
I am having trouble setting the dbkey of an output data set. The input and
output, respectively, is shown below. I copied this from the bowtie_wrapper.xml
but the difference is that I do not have a condition on selecting the
reference genome. My tool requires a .loc file. The tools completes
Hi,
Recently I moved my locally installed Galaxy from a local hard drive to an
NFS mounted hard drive, when I run some tools, I go the following error from
the log file:
Job output not returned by PBS: the output datasets were deleted while the
job was running, the job was manually dequeued or
Is there a list of associated attributes such as $input.ext, $input.dbkey and
$input.id?
Ilya Chorny Ph.D.
Bioinformatics Scientist I
Illumina, Inc.
9885 Towne Centre Drive
San Diego, CA 92121
Work: 858.202.4582
Email: icho...@illumina.commailto:icho...@illumina.com
Website:
We've digested this topic a bit here at Galaxy Central, and agree that at some
point ( maybe soon for very basic functionality ) we need to provide support
for new data types in tool shed repositories. It would be very helpful ( and
significantly speed up the development process ) if the
Would it be difficult to add the url as an attribute of the input and output
parameters ($param.url)? If you point me to where these values are set, I can
try to make the changes to the code.
Thanks,
Ilya
-Original Message-
From: galaxy-dev-boun...@lists.bx.psu.edu
You mention that you moved it to an NFS volume - but it seems you also moved to
a grid configuration using PBS?
If that's the case, what you are seeing might be an issue with NFS attribute
caching or write caching, which causes files created from one machine to not
appear until some time later
Well, I didn't move it to a grid configuration using PBS recently, it was
already using a grid configuration with PBS before I moved it to the NFS
volume and no such an error ever happened :) So it must be related to NFS.
Thanks for you great suggestions! I will try them out and see how they
Dannon Baker wrote:
Oren,
I've moved this thread over to the galaxy-dev mailing list since it deals
with a local installation. Users on this list are more likely to have an
answer for this type of question.
That said, we don't officially support running Galaxy under Cygwin (or
Oren Livne wrote:
Dear Nate,
I've been doing exactly that. What's driving me crazy is that every
second compile (bx_python, numpy, pysam) runs into a Cygwin DLL
remap failure that cannot be resolved with /bin/rebaseall. So any
advice on how to get rid of that would be great. Right now it's
Dear Nate,
I've been doing exactly that. What's driving me crazy is that every
second compile (bx_python, numpy, pysam) runs into a Cygwin DLL remap
failure that cannot be resolved with /bin/rebaseall. So any advice on
how to get rid of that would be great. Right now it's failing in the
Hello all,
Further to recent discussions about dealing with large
FASTQ files, and the short term advantages of gzipped
FASTQ as a filetype in Galaxy (or gzipped files in general,
https://bitbucket.org/galaxy/galaxy-central/issue/666/ ), we
also discussed the merits of unaligned BAM files.
It
So we came up with a work around and I wouldn't mind getting your opinion on
it. Specifically with respect to passing cookie_path. I could not figure out
how to get the proxy prefix from the universe_wsgi.ini file via the $__app__
call. Also you mention in the wiki the the $__app__ may get
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