Hi everyone,
Is there a Galaxy XML tool wrapper XSD ?
Thanks,
Pierre
--
Pierre Pericard
IE CDD - Projet Peptisan
Service Informatique et Bio-informatique (SIB)
Station Biologique de Roscoff
CNRS - UPMC
Place Georges Teissier
CS 90074
29688 ROSCOFF CEDEX
FRANCE
Tel : (+33) 2 98 29 56 46
Hi all,
Are all the data files in .loc files needed to download and put to the right
directory when we install our local galaxy?
thaks
shenwiyn
shenwiyn___
Please keep all replies on the list by using reply all
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On Sat, Feb 16, 2013 at 9:41 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
Thanks for your thoughts on this. I've created the following Trello card for
this enhancement.
Hello all,
Although they are these days also offering XML for many tools,
the NCBI still make heavy use of the older ASN.1 file format
(both as plain text and binary). This crops up in BLAST (e.g.
as the BLAST archive format, or as dustmasker output), in
the Entrez Utilities (e.g. for sequence
Hi Peter, see below...
On Feb 19, 2013, at 5:10 AM, Peter Cock wrote:
On Sat, Feb 16, 2013 at 9:41 PM, Greg Von Kuster g...@bx.psu.edu wrote:
Hi Peter,
Thanks for your thoughts on this. I've created the following Trello card
for this enhancement.
On Tue, Feb 19, 2013 at 11:39 AM, Greg Von Kuster g...@bx.psu.edu wrote:
On Feb 19, 2013, at 5:10 AM, Peter Cock wrote:
Yes, the complete directory hierarchy and content of the original
repository revision is preserved when it installed into Galaxy.
Based on a sample of one, it seems the
On Tue, Feb 19, 2013 at 6:32 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Would a pull request implementing this be acceptable?
Yes. My understanding is that ASN is a completely flexible metaformat,
like XML, and so should be under either Text or Data, with appropriate
subtypes defined for
On Tue, Feb 19, 2013 at 3:39 AM, Pierre Pericard
pierre.peric...@sb-roscoff.fr wrote:
Is there a Galaxy XML tool wrapper XSD ?
No, but if anyone would like to make such a schema we would be happy
to include it.
--
James Taylor, Assistant Professor, Biology/CS, Emory University
Hey Pierre,
If you are going to write one and want a starting point, here is the
schema I used for incorporating Galaxy tools into a Java web service
workflow framework called TINT:
https://github.com/jmchilton/TINT/blob/master/projects/TropixGalaxy/schema/galaxy.xsd
It is mostly a subset of
On Tue, Feb 19, 2013 at 2:00 PM, James Taylor ja...@jamestaylor.org wrote:
On Tue, Feb 19, 2013 at 6:32 AM, Peter Cock p.j.a.c...@googlemail.com wrote:
Would a pull request implementing this be acceptable?
Yes. My understanding is that ASN is a completely flexible metaformat,
like XML, and so
hi:
When we running a local installation of Galaxy,there are some reference
dataset ,such as Human Feb. 2009 (GRCh37/hg19) (hg19),A. gambiae Feb. 2003
(IAGEC MOZ2/anoGam1) (anoGam1),and so on.Shall we download these datasets
and save in our computer ?
This is my first use Galaxy,it is very
Hello all,
I was wondering how people keep track of the available file format
definitions in the tool shed(s)? For core file types defined in Galaxy,
I can just view the datatypes_conf.xml file and/or the classes in
lib/galaxy/datatypes/ - but how can I do something similar on a
Galaxy Tool Shed?
Hi Peter,
This is not yet available, but something I've been planning to do for quite a
while. I've opened the following Trello card for this. I'm not exactly sure
yet how this will be implemented as I haven't thought this completely though.
Of course, ideas from the community are always
On Feb 14, 2013, at 7:26 AM, James wrote:
Hi Nate,
Thanks for your reply,
I guess the idea is that the job is prepared in the interface which lets a
user select
the grid. This is currently located in my galaxy instance as a if statement
in the
default job dispatcher. Just before it
On Tue, Feb 19, 2013 at 5:08 PM, Nate Coraor n...@bx.psu.edu wrote:
On Feb 19, 2013, at 11:23 AM, Peter Cock wrote:
Hi all,
I've got an hg puzzle, can anyone on the Galaxy team explain the
cause of this and what action I can take to avoid it?
Starting with a clean checkout,
$ hg clone
On Feb 19, 2013, at 12:18 PM, Peter Cock wrote:
On Tue, Feb 19, 2013 at 5:08 PM, Nate Coraor n...@bx.psu.edu wrote:
On Feb 19, 2013, at 11:23 AM, Peter Cock wrote:
Hi all,
I've got an hg puzzle, can anyone on the Galaxy team explain the
cause of this and what action I can take to avoid
On Tue, Feb 19, 2013 at 5:26 PM, Nate Coraor n...@bx.psu.edu wrote:
On Feb 19, 2013, at 12:18 PM, Peter Cock wrote:
Nate wrote:
Hi Peter,
This is due to the annoying way in which Mercurial handles symlinks. We're
going to graft the changesets that caused this up to stable shortly, but in
Jorrit,
Thank you for uncovering that issue, I've commited a fix in the stable
branch of galaxy-central at 8887:d5896e8a60fa. To apply that changeset,
you'll need to run the following commands from your Galaxy directory:
$ hg pull -b stable https://bitbucket.org/galaxy/galaxy-central/
$ hg
Il giorno mar, 19/02/2013 alle 14.15 +, Peter Cock ha scritto:
On Tue, Feb 19, 2013 at 2:00 PM, James Taylor ja...@jamestaylor.org wrote:
On Tue, Feb 19, 2013 at 6:32 AM, Peter Cock p.j.a.c...@googlemail.com
wrote:
I think it could make sense to define generic 'asn1' and
'asn1-binary'
Hello,
thanks, I managed to run the instances by using BioCloudCentral on the same
SecurityGroup and Keys I already set up, which were fine. For some reason
pointing the browser to the address provided by Amazon, as described in your
Wiki CloudMan thread, did not work, but finally I found some
Stefano,
Could you clarify what you did differently? The public URL provided
by Amazon *should* be the primary interface to your cluster.
-Dannon
On Tue, Feb 19, 2013 at 12:55 PM, stefano cardinale
cardinale.stef...@gmail.com wrote:
Hello,
thanks, I managed to run the instances by using
On Tue, Feb 19, 2013 at 6:45 PM, Nicola Soranzo sora...@crs4.it wrote:
Il giorno mar, 19/02/2013 alle 14.15 +, Peter Cock ha scritto:
On Tue, Feb 19, 2013 at 2:00 PM, James Taylor ja...@jamestaylor.org wrote:
On Tue, Feb 19, 2013 at 6:32 AM, Peter Cock wrote:
I think it could make sense
Hi,
I have my own local galaxy installed and things are great. However, I am
running of space, is there a better way to free space from the GUI? I have
been deleting sets/files from my history but it looks like the Usage still
going up. I manually run the following scripts but still nothing
you can go to options. then click on show deleted datasets. then this will make
appear all datasets that have been deleted but are not yet removed from the
disk.
You will see something like this: This dataset has been deleted. Click here to
undelete or here to immediately remove it from disk.
Hello all,
There are a couple of things going on with the GMOD
Projecthttp://gmod.org/wiki/ that
the Galaxy Community might be interested in. If you aren't familiar with
GMOD, it is a federation of open-source projects and tools that enable
visualizing, annotating, managing, and analyzing
Thank Alfonso,
Where is the Options menu though? I do not see anything called Options.
Thank you
-Original Message-
From: Alfonso Garrido-Lecca [mailto:alfonso.garrido-le...@colorado.edu]
Sent: Tuesday, February 19, 2013 2:54 PM
To: Hakeem Almabrazi; Galaxy Dev
Subject: Re:
Thanks guys,
I will give it a try.
Cheers,
D
On Wed, Feb 20, 2013 at 12:40 AM, Nate Coraor n...@bx.psu.edu wrote:
Thanks Dannon. One more tip: If you commit your changes on the default
branch, you will need to merge them with stable, i.e. `hg update
release_2013.02.08` followed by `hg
Hi,
I am trying to setup my galaxy system to allow jobs to be submitted as the
real user, since people want to keep an eye on their job on the cluster
sometimes and they have no ideas which ones are theirs.
I tried the approach on the wiki here:
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