I have been taking a look at Galaxy and playing with it a bit. I have also
watched several of the great tutorials. One that was particularly relevant
to what I want to do was the one on SNPs. But, in addition to finding out
what type of genomic region a SNP lies in e.g. intron or exon, I also want
to determine, for SNPs that are in coding regions, whether they are
snynonymous or non-synonymous. Is there a way of doing this in Galaxy?
I have had a really good hunt in the Tools menus but I can't find anything.
Any help much appreciated.
Tim Hughes PhD (http://digitised.info)
Medical Genetics Department
Oslo University Hospital Ullevål
We have a local galaxy install at our facility that is running on a VM
machine with an allocated memory of 2gigs. I have a user that has been
trying to upload a ~6gig fastq file to galaxy for the past couple of days
within our same subnet. She tried submitting the upload but the next day it
still wasn't finished uploading, so I told her to cancel the upload and try
again. The same problem occurred the second day after a day of trying.
Should galaxy be able to support an upload of this size?
since two days, when trying a fresh galaxy install it hangs.
I don't know if it has to do with my setup or internet connection (fc8,
x86_64, Python 2.5.1).
hg clone http://bitbucket.org/galaxy/galaxy-central galaxy-central
after sh setup.sh
it stalls at:
but after some time it proceeds:
One of the python eggs necessary to run Galaxy couldn't be downloaded
automatically. You may want to try building it by hand with:
python scripts/scramble.py Mako
after ./run.sh there is no output for some time, then:
Traceback (most recent call last):
File "./scripts/paster.py", line 24, in <module>
pkg_resources.require( "PasteScript" )
File "/home/tamir/dl/galaxy/lib/galaxy/eggs/__init__.py", line 558, in
if not egg.fetch():
File "/home/tamir/dl/galaxy/lib/galaxy/eggs/__init__.py", line 101, in fetch
raise EggNotFetchable( self.name )
and this is of course the end of it.
So I wanted to add in the number of sequences in a file, which is
something that is often requested. My initial thought was to add a
tool, which I could do, but then I thought that this was metadata that
should probably be added to any record based class. So I then thought
that I would find the code that set up the file size information in
the history column and copy that, but looking at the source, that goes
in the blurb (e.g. sequence.Fasta).
So here are my questions:
* how can a user see the metadata, as this is distinct to the blurb/peek?
* why isn't the file size implemented as a piece of metadata?
Dear Galaxy team:
I was recently introduced to Galaxy framework by my colleagues in
Singapore. I am very impressed with it and want to start using it right
away. Now the questions are whether I should use the public server or
attempt a local installation. I understand this depends on how we intend
to use the system. What I would like to get advice from you is the
security of using public server. If I setup my login and start using the
system for private data, say high throughput sequencing data, who else
could possibly see my data without my knowing it?
As you know, pharmaceutical companies traditionally have a tendency
to setup everything if possible locally. With the recent data explosion,
it is becoming more and more unrealistic to maintain internal copies of
public tools and data. More importantly, I feel it could be a waste of
resource and could introduce unnecessary data provenance problems. From
the server maintenance standpoint, how much effort is needed to keep the
framework up and running? Do you encourage pharmaceutical companies to use
your public server? Have you thought about carving out a section of your
server to private users for a fee? I anticipate one or two people to use
the server initially for a period of time when we initially get the data
and afterwards occasionally use it. I hope to avoid local installation if
Jian Wang, PhD Informatics Eli Lilly & Co. Phone: 317
655 3496 E-mail: jian.wang(a)lilly.com
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So you can have tabular datasets, and you can add a datatype that
subclasses tabular and adds column definitions.
Is there a way of using tabular data with column headings without
defining the datatype, i.e. getting galaxy to recognise that first
line is a header and should be used as column titles?