Hello all,
one of my users encounters a strange error with the GATK tool Unified
Genotyper. At the end of the message you see the original error report. The
problem there was that the reference genome is missing. The tool was run as a
part of a bigger workflow, but I double checked the
Hi Edward,
you need to enter:
hg clone https://bitbucket.org/galaxy/galaxy-dist/
without the %. That usually indicates a shell.
Mercurial (the 'hg' program) should also be installed.
Ciao,
Bjoern
Both responses worked for checking python version, but trying to
download gave an error:
Hi Edward,
Sorry, the https is probably also a problem. I thought about
commenting about that before, but was wasn't sure about how much help
you would need exactly or if you were logged into bitbucket or not. So
please use this:
prompt$ hg clone http://bitbucket.org/galaxy/galaxy-dist
Update (and a post to both lists!)
Nate pointed me to the real problem. https/http isn't a problem at
bitbucket anymore. The issue is where you are installing (/etc) and
write permissions. But, it is not recommended anyway. You will want to
install in your home directory. To get there, type:
Hi Diana,
Galaxy itself will run on any recent MAC with the basic requirements
(python, mercurial, etc.). The standard set-up isn't computationally
intensive at all.
What makes a difference are the tools you intend to use, the size of the
data (genomes, datasets, libraries), the volume of
Hello Ted,
Workflows are included in the Galaxy Main Tool Shed
http://toolshed.g2.bx.psu.edu/
-- Search for workflows
Documentation is in this wiki (see #22, 23, 24):
http://wiki.g2.bx.psu.edu/Tool%20Shed
Other current information about workflow development can be found in the
Both responses worked for checking python version, but trying to download gave
an error:
Install Galaxy on Mac OS10.7
1. Open Applications/Utilities/Terminal.app
2. Check Python version by pasting in python -V, no quotes, and hit return
response = Python 2.7.1
3. Get Galaxy by pasting in
I was wondering if anyone could comment on how memory/computational intensive a
local instal of Galaxy is? What type of computer (especially Macs) is needed
for a local install to run fairly well?
Thanks for any info--- Diana
**
Diana Cox-Foster, Professor
Hi Jen,
Yes, it is best to assume I know nothing about programming. I installed
Mercurial, but don't know how to check that it was successful other than it
said so. Removing % helped, but said I do not have permission:
Install Galaxy on Mac OS10.7
1. Open Applications/Utilities/Terminal.app
2.
Thanks Jen, Hans, and Scott,
I have it running on my laptop now and here are the steps I followed:
Install Galaxy on MacBook Pro OS10.7.4 (08-10-2012)
• Install Mercurial http://mercurial.selenic.com/wiki/
• Open Applications/Utilities/Terminal.app
• Confirm Mercurial
Hi Jen,
I know we are using Mercurial for Galaxy's own source code.
Is there a way for Galaxy to store and retrieve workflows from Mercurial?
Thanks,
Ted
UCSC CBSE
On Aug 10, 2012, at 1:06 PM, Jennifer Jackson wrote:
Hi Diana,
Galaxy itself will run on any recent MAC with the basic
Jen - Getting Closer! - But not there yet.
Getting Galaxy seems to have worked. Here is the last line from Terminal:
mbio-edt:~ edwardturk$ cd
mbio-edt:~ edwardturk$ hg clone http://bitbucket.org/galaxy/galaxy-dist
warning: bitbucket.org certificate with fingerprint
Dear Galaxy team,
I am currently running a RNA-seq experiment and wishing to use Galaxy to do all
analyses on a public server.
My genome (Eucalyptus grandis: http://www.phytozome.net/eucalyptus.php) is not
on the genome list.
Could you please make it available?
Many thanks
Saro
Hello Saro,
We had considered adding this genome in the past, but it had specific
usage requirements that we were not able to support/display in a way
that will meet the criteria set by the data owners. This has not changed.
In addition, we also now require that genomes are submitted to NCBI
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