Jim;
Thanks for the interest in the nglims code. This currently needs some
work to get back working cleanly with the latest versions of Galaxy
since the Javascript libraries changed and jWizard seems unhappy with
the latest jQuery.
So the current status is still, try it out since it needs some
sequence' menu wasn't there under the Lab tab. I watch the video you posted
at the youtube, but still couldn't find it. Do you know what I miss here?
Thanks.
Best,
Peter
-Original Message-
From: Brad Chapman [mailto:chapm...@50mail.com]
Sent: September-18-13 8:44 PM
To: Peter Huang
your needs before investing time in it.
Sorry the process isn't easier and hope this helps,
Brad
-Original Message-
From: Brad Chapman [mailto:chapm...@50mail.com]
Sent: September-17-13 9:47 PM
To: Peter Huang; galaxy-user@lists.bx.psu.edu
Subject: Re: [galaxy-user] add nglims
Peter;
I maintain nglims as a fork of galaxy-central, syncing back to the main
repository regularly:
https://bitbucket.org/chapmanb/galaxy-central
This was an easier approach than trying to keep a set of patches up to
date. Hope this helps,
Brad
Hi Brad,
I am curious if you could tell me
.
Should I delete cm.tar.gz and rename cm.tar.gz_2012-07-24 to cm.tar.gz?
-Greg
On Tue, Jul 24, 2012 at 9:45 PM, Brad Chapman chapm...@50mail.com wrote:
Greg;
Did you try rebooting or restarting the cluster? The error logs complain
about SGE due to the original older CloudMan but it seems like
: [Errno 2] No such file
or directory: '/mnt/cm/post_start_script'
18:09:23 - Updating CloudMan application source file in cluster's
bucket 'cm-xxx'. It will be automatically available the next this
cluster is instantiated.
Thanks again,
Greg
On Mon, Jul 23, 2012 at 3:49 PM, Brad Chapman
Greg;
I created a new Galaxy instance (probably around early July) with the
web launcher (https://biocloudcentral.herokuapp.com/launch).
I've been coming back and re-using it since then. However for the
past week at least I haven't been able to launch new nodes. They show
up as red on
://www.ajaxload.info/
The Javascript function could just remove or hide the icons once the
final info is loaded.
-Greg
On Thu, Jan 26, 2012 at 9:03 PM, Brad Chapman chapm...@50mail.com wrote:
Greg;
As you dug into, the javascript function should keep refreshing and
checking the state
Greg;
As you dug into, the javascript function should keep refreshing and
checking the state until the information is available from the EC2
console, and then fill it in. This does work for me as intended on
Firefox 9.0.1 and Chrome. It normally takes a minute or so for the
server information to
Enis and Greg;
This sounds like the availability zone issue. I am assuming you are
restarting the same cluster (i.e., using the same name) and the instance
that gets created may be created in a zone different from the one that
the
volume from the previous instantiation of the
Greg;
I'm almost positive I originally started the instance via
BioCloudCentral, and I always use Large. I've been exclusively using
BioCloudCentral for a few weeks now.
I hadn't noticed this issue until yesterday. I can definitely do
whatever you need if you want to dig into the issue
Greg;
I've asked some questions about sharing an instance but it doesn't
seem to be working the way I'm expecting (Unfortunately I'm also new
to Amazon EC2/S3 so that may be part of my difficulty). I'm thinking
maybe if I can explain what I'm trying to do, you guys could tell me
the best
Colleen;
Yoy definitely only want to select a single security group: the CloudMan
one. Selecting multiple groups like uses the most conservative settings
in the union of the groups, so won't have the right ports open for CloudMan.
The ami I've been mainly using is ami-da58aab3 (although I've
Colleen;
I am having trouble setting up access to the galaxy cloud instance
and may have missed something in the tutorial (I am following this
one:http://wiki.g2.bx.psu.edu/Admin/Cloud)
I am able to launch the instance
I can access it through ssh, but when I try to access it through
Peter and Guru;
[Computing GC]
I'll be working with simple sequence files (FASTA, or even FASTQ,
SFF, etc) rather than BED files, but I'll keep that in mind.
Emboss has some utilities that do this. infoseq and geecee, and
there are also programs for exploring CpG islands:
Ying and all;
Nice discussion and lots of great ideas. One other approach is to generate
bigWig files. You can serve these directly from Galaxy and they have
the same advantages as BAM files; they are compressed and individual
regions that be fetched on demand by UCSC.
This tool in the community
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