Galaxy source repository change
by Nate Coraor
Hello,
If you simply use the Galaxy Main or Test sites hosted at PSU, you can
safely ignore this message. It pertains to people who've checked out
their own copy of Galaxy for development or local use.
Galaxy development has recently moved source control systems, from
Subversion to Mercurial. This means that anyone using a local copy of
Galaxy will need to make some changes to be able to download future updates.
The preferred method of obtaining Galaxy source is through Mercurial
directly (the 'hg' command):
hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist
Tarballs are also available via the zip/gz/bz2 links here:
http://www.bx.psu.edu/hg
And the repository is mirrored in Subversion here:
svn co http://www.bx.psu.edu/svn/galaxy galaxy_dist
Unfortunately, modifications to local copies of Galaxy will need to be
transferred from your old checkout to the new checkout.
Please let us know via <galaxy-bugs(a)bx.psu.edu> of any issues. Thanks,
and thank you for using Galaxy.
--nate
12 years, 1 month
Importing features from BioMart
by Alexandre Gattiker
Hello,
I would like to import features from BioMart into galaxy. However the
'embedded' BioMart view yields an HTML table. How do I convert that to
GFF or BED?
Best regards
--
--------------------------------------------------------
Alexandre Gattiker Bioinformatics & Biostatistics Core Facility
EPFL School of Life Sciences / Faculté des Sciences de la vie FSV
http://people.epfl.ch/Alexandre.Gattiker
12 years, 1 month
Synteny
by Claudio Casola
Hello,
I found Galaxy extremely helpful in the past months and I have an
issue that could again be solved using your wonderful platform.
I am playing with a bunch of sequences (genome coordinates) from the
human genomes that I obtained from some blast searches.
I would like to see if these exact sequences are shared by (in
synteny with) chimp, orang and macaque.
I got MAF blocks from Galaxy and played with them, but I don't see an
easy solution.
It would be great if you have some suggestion about how to work with
synteny using Galaxy, if possible.
Thanks a lot!
Claudio Casola
Postdoctoral fellow, Hahn Lab
Department of Biology
1001 East Third Street
Bloomington, IN 47405-3700
Indiana University
812-856-7016
ccasola(a)indiana.edu
12 years, 2 months
Lift-Over update with orangutan assembly
by Claudio Casola
Hello,
Is there any chance to have the orangutan assembly included in the
Lift-Over menu any time soon? That would be great!
Thanks,
Claudio Casola
Postdoctoral fellow, Hahn Lab
Department of Biology
1001 East Third Street
Bloomington, IN 47405-3700
Indiana University
812-856-7016
ccasola(a)indiana.edu
12 years, 2 months
Interfacing galaxy with a local copy of the UCSC genome browser
by Tim Yu
hi there,
We've just set up a local instance of Galaxy to serve as a framework
for adding custom tools. We also have a local server running a copy
of the UCSC genome browser with our own data on it. Is there a way to
configure Galaxy to interface with our in-house UCSC server, instead
of (or in addition to) the central site?
Is this, by the way, the approved place to direct such questions? I
didn't see an email address for support on the main site or wiki.
Thanks!
Tim Yu
12 years, 2 months
How to get output from Galaxy
by i rezwan
Hi,
I am a very new user at Galaxy. I have downloaded the Galaxy and am
running it in my computer locally. Actually I am developing a script
in python which I want to integrate with Galaxy on TEST basis. I can
add the tool and run the program very well by following Galaxy
tutorials.
But the one problem that I am facing is, I don't know how to get an
output from Galaxy. I will prefer to get the output in a
text file locally mentioned by user (to make it a bit more user
friendly). I have examined through the example .xml file and also seen
the galaxy screencast, but still unable to generate an output file for
my tool.
I'm using browser: mozilla 3.0 and OS: ubunutu linux.
Thanks in advance.
Regards
/Faisal
--
Faisal Ibne Rezwan
BioComputation Group, Rm # 1E114
Science and Technology Research Institute
University of Hertfordshire
College Lane Campus
Hatfield, AL10 9AB
UK
Tel +44 (0)1707 286356
12 years, 3 months
