Hello all,
I was looking at Edward's updated HMMER wrapper on the toolshed,
http://toolshed.g2.bx.psu.edu/
There is a preview offered for the (simple) hmmpress.xml only, giving
the impression that Edward's repository isn't very useful.
Why isn't anything shown for the more complex hmmer.xml? If
Hi,
I have the same error message for multiple tools (GFFtoBED,
BEDtoBIGBED,BAMtoSAM,...):
/from galaxy import eggs
ImportError: No module named galaxy
It's happening only since the last upgrade, do you know what is going wrong?
Thanks,
Alban
/
--
Alban Lermine
Unité 900 : Inserm - Mines
Hi Peter,
Here is the error produced by attempting to load the hmmr.xml tool config into
the tool shed. With regard to tool validity, the definition of a valid tool in
the tool shed has always been restricted to the tool properly loading in a
Galaxy instance. If a tool is not valid, it will
On Mon, Mar 19, 2012 at 1:28 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
Here is the error produced by attempting to load the hmmr.xml tool config
into the tool shed. With regard to tool validity, the definition of a valid
tool in the tool shed has always been restricted to the tool
Hello,
My instance of galaxy is running on an sshfs mount.
The problem comes when I set the new_file_path in the universe_wsgi.ini
to be a folder within that sshfs.
When I upload something, the hard link in the mkstemp_ln function fails
because of apparent limitations of sshfs with hard links. It
Hi,I have run into an issue with a tag being duplicated hundreds of times each time I open, edit or clone a workflow.I have tried to manually remove them, but each time the tag gets inserted somehow and duplicated each time I edit the workflow.By now there are hundreds of copies of the tags at it
It seems that trackster does not know how to display INTERVAL files?Is that true? Surely there is an easy way to support those kinds of simple files without having to convert them?Am I missing something?I also don't seem to be able to convert an interval file into a BED file?Thanks,Thon
Oh wait..It's in the info section...Weird place for a conversion tool but it is there :)On Mar 19, 2012, at 12:02 PM, Anthonius deBoer thondeb...@me.com wrote:It seems that trackster does not know how to display INTERVAL files?Is that true? Surely there is an easy way to support those kinds of
Thon,
It seems that trackster does not know how to display INTERVAL files?
Is that true?
Yes, this is currently a limitation. However, most of the work is done that is
necessary to make this happen, so it should be done soon, definitely in the
next month or two.
Surely there is an easy way
I'm writing some tools to integrate NCBI data
resources with Galaxy. I have two questions.
The first is simple. I want to write a tool for a long-running
process that is handled by some other scheduler, and that produces
its own job ids. Some web services,
Greg,
Regarding the performance of different types of instances, I came across
this and thought you might potentially find it useful:
http://cloudharmony.com/benchmarks
Enis
On Mon, Mar 19, 2012 at 7:49 PM, Greg Edwards gedwar...@gmail.com wrote:
Enis,
Thanks. Will try that re the storage.
Hi Enis, Greg,
I've taken stuff from my this email, and previous conversations with Enis
and put it in the wiki:
http://wiki.g2.bx.psu.edu/Admin/Cloud/CapacityPlanning
Please feel free to update/correct/enhance.
Dave C.
On Mon, Mar 19, 2012 at 2:58 PM, Enis Afgan eaf...@emory.edu wrote:
Just one extra thought on this-- If you leave your instance up all the time it
may be worth looking into having a reserved micro instance up as the front end
(cheap, or free, with your intro tier) with SGE submission disabled. Then,
enable autoscaling(max 1) of m1.large/xlarge instances.
Hi there,
I am new to Galaxy and I've just recently learned how to integrate a Perl
script to it. Now, my code uses the input file's name as a header for a
column in the output. When I ran it in Galaxy, I did get the filename, but
it's the one ending in .dat (actually, I got the entire path of
Dear galaxy,
I'm trying to install galaxy on a 64bit Debian (5.0) Lenny server with
python2.5.2. When running %sh run.sh, the fetch_eggs completed
successfully. However, I have problem with running galaxy instance. I've
posted the error messages below.
Traceback (most recent call last):
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