*Register for the March 2011 GMOD Meeting (
http://gmod.org/wiki/March_2011_GMOD_Meeting) by this Friday, Feb 18, and
save over 15%.*
The March meeting is part of GMOD Americas 2011 (
http://gmod.org/wiki/GMOD_Americas_2011), an event that includes Satellite
Meetings, a GMOD Course (already full), and for the first time, an
"Introduction to GMOD" session the night before the meeting for GMOD
newcomers. GMOD Americas 2011 events are being held at the US National
Evolutionary Synthesis Center (NESCent) in Durham, North Carolina, United
Also, if you have a topic you want to discuss at the meeting, please send it
to Scott Cain <scott(a)scottcain.net> ASAP so he can get you on the program.
GMOD is the Generic Model Organism Database project, a collection of
interoperable open-source software components for annotating, visualizing,
managing and analyzing biological data. GMOD is also an active community of
software developers and biologists addressing common challenges with their
The GMOD suite includes widely used tools such as GBrowse and JBrowse (and
WebGBrowse) for genome browsing, Apollo and MAKER for genome annotation,
GBrowse_syn and CMap for comparative genomics visualization, Chado, BioMart
and InterMine for data integration, management, and querying, and Galaxy and
Ergatis (and ISGA) for data analysis.
*As with previous GMOD meetings, this meeting will have a mixture of project
talks, component talks, and user talks. Our guest speaker is Dr. Eric Stone of
North Carolina State University. Dr. Stone will talk about his experience on
the "Drosophila Genome Reference Panel," a project that is sequencing and
annotating almost 200 inbred lines.
The agenda is driven by attendee suggestions, and you are encouraged to add
your suggestions now. For an idea of what happens at a GMOD meeting, see the
writeup of the September 2010 GMOD Meeting. GMOD meetings are an excellent
way to meet GMOD developers and users and to learn (and affect) what's
coming in the project.
*Registration for the March 2011 GMOD Meeting is
$80 on or before February 18
$95 after February 18
Please register early, both to save money, and ensure a spot. You are also
strongly encouraged to submit a talk and/or sign up for (or propose) a
Satellite Meeting. Details on transportation, suggested lodging, and other
logistics are on the GMOD Americas 2011 page.
This meeting, and all GMOD Americas 2011 events, are jointly sponsored by
NESCent and the Galaxy Project.
Hope to see you in North Carolina!
PS: And I hope to see you in the Netherlands as well! *The abstract
submission deadline for the Galaxy Community Conference is Feb 28.* See
Last day we upgraded our galaxy service computing cluster nodes operating
system from Ubuntu hadry to lucid 10.4. We updated python eggs and now
getting an Warning message, it apparently kills the galaxy jobs. Warning
message as follows:
/home/abc/galaxy/lib/galaxy/eggs/__init__.py:332: UserWarning: Unbuilt
egg for pytz [unknown version] (/usr/lib/python2.6/dist-packages)
env = pkg_resources.Environment( platform=pkg_resources.get_platform() )
>From the warning message I can see that the problem with unbuilt egg for
pytz module. Before approaching you I googled the same and got a good thread
which explains similar kind of issues (
followed #9 from TJ and made a work around and unfortunately no luck. Does
anyone had a problem with this before, if yes I like to hear from you that
how do u managed to get rid of the warning message.
Vipin T S
Friedrich Miescher Laboratory
of the Max Planck Society
Spemannstrasse 39, 72076
We are looking at integrating some tools into Galaxy for a domain
where many of the existing programs are Windows only. My desire is to
write tool files and have the certain jobs run remotely on a Windows
host (our Galaxy servers are Linux). It wasn't clear how to do this with
the existing job runners since they all seem to require a shared file
system and absolute file paths that are the same on the Galaxy server as
they are on the remote execution hosts.
I developed a new job runner that allows for the remote execution
of jobs that also rewrites paths and stages files as part of the job
execution. There is a server application that needs to be running on the
remote machine (*nix or Windows). This application is likely easier to
setup/configure than SGE/PBS/etc... because it is a simple Python paste
application, with just a few configuration options. There may be valid
use cases for this approach for non-Windows applications as well - if
you would like a lighter weight server component on the remote system,
if shared file systems are impossible/impractical, etc....
The path rewrites are not going to cover every possible way an
absolute path can sneak into the execution, so this is only useful for a
subset of tools. But it does handle normal file inputs and outputs,
config files, and scripts in the tool definition directory. I welcome
input/advice on this approach or the implementation. If there is any way
I can improve the code base to the point where it can be included in
galaxy-central I would be more than happy to make the desired changes.
If not, it is out there for people to use if they have a similar use case.
The server application as well as a patch to add the runner/client
to a galaxy-central installation can be found at:
Thanks for your time,
University of Minnesota Supercomputing Institute
I have just installed Galaxy and am trying to configure it to allow
display of data on my local installation of GBrowse.
I have edited tool-data/shared/gbrowse/gbrowse_build_sites.txt (species
As well as universe_wsgi.ini (gbrowse_display_sites = species)
However I do not see a link in history items after I stop and start the
Is there something else I'm missing?
Thanks in advance for your help,
I've been doing some testing with a Galaxy instance running on my laptop for some tools we are developing. I am uploading a file into Galaxy from a URL to use as test input (~1.5GB tabular) I can download this file to my laptop in ~30 seconds with wget, while if I pull from the same URL into Galaxy it takes about 30 minutes. I set the file type so Galaxy did not have to auto-detect.
This seems very slow considering it only takes about 30 seconds to get the file over the network and write it to disk. What is Galaxy doing that makes this file upload so slow? We also tried defining our own datatype (data, not tabular with the thought that maybe Galaxy tried to examine tabular files), but it is still very slow. In production our input files will grow to be much larger than this (although we'll probably abandon tabular for a more compact binary format by then).
Glen L. Beane
The Jackson Laboratory
Phone (207) 288-6153
I seem to remember there being talk of a parameter you can set in the
universe file that allows you to limit the size of files for which
metadata is set when galaxy uploads a file.
Was this put in to production?
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
Trying to install a local copy of Galaxy for evaluation. Downloaded
the "stable" version using:
hg clone https://bitbucket.org/galaxy/galaxy-dist
I am installing it on a Centos 5 x86_64 Linux kernel which has python
2.4.3 installed. When running "sh setup.sh" the installation stops
with an error building the "python_daemon" egg. In checking, it is
trying to download/build python_daemon 1.5.5 (specified in the
eggs.ini). This version of python_daemon uses syntax that depends on
python >= 2.5. Your "README" indicates....
Galaxy requires Python 2.4, 2.5 or 2.6. To check your python version, run: ...
Does Galaxy still run under python 2.4?
(PS: I have lots of Linux/Perl experience, but virtually no python expertise.)
//=\ John Powell, CAPT, Ret. USPHS Phone: (301) 496-2963
\=// Building 12A, Room 2033 FAX: (301) 402-2867
//=\ National Institutes of Health
\=// Bethesda, MD 20892-5624 Work: jip(a)helix.nih.gov
//=\ Personal: jpowell(a)erols.com
//=\ BioInformatics & Molecular Analysis Section-BIMAS/CBEL/CIT/NIH
Sonali Amonkar wrote:
> I'm trying to install and run galaxy-dist-8729d2e29b02 on a Linux RHEL 5.5 box. This machine has no direct access to the Internet. I followed the steps listed on the page https://bitbucket.org/galaxy/galaxy-central/wiki/Config/Eggs to download the eggs offline and placed them in the correct location.
> Now when I try to run Galaxy (sh run.sh), it appears to be stuck trying to contact http://184.108.40.206 - this was seen through netstat.
> [workflow@vm-ps4121 galaxy-dist]$ netstat -antp | grep tcp
> (Not all processes could be identified, non-owned process info
> will not be shown, you would have to be root to see it all.)
> tcp 0 1 10.88.176.157:44233 220.127.116.11:80 SYN_SENT 5796/python
> Why does galaxy try to connect to this server when all the eggs are already updated?
> My questions are:
> 1. Can galaxy-dist-8729d2e29b02 can be run on a box with no Internet access?
> 2. How does one enable this no-Internet-available setting in galaxy-dist-8729d2e29b02?
There were two bugs which were preventing all of the eggs from being
downloaded by the egg packaging script. These are resolved in
5038:559a9ad2844d. This changeset is available in our in-development
repository. It will be in the distribution repository at some point
within the next few weeks, or you can pull the bleeding edge directly
% hg pull -u http://bitbucket.org/galaxy/galaxy-central/
> Thank you for your time.
> Sonali Amonkar
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> galaxy-user mailing list
In addition to the Galaxy organized workshop proposal that I just sent out,
there is another workshop proposal being created that may be of interest to
anyone working in a sequencing center.
See below for details. Their deadline is tomorrow (Thursday) as well.
Contact Brent if you have questions.
---------- Forwarded message ----------
From: Richter, Brent G. <BRICHTER(a)partners.org>
Date: Tue, Feb 8, 2011 at 7:59 AM
Subject: [bioinfo-core] request for speakers: ISMB 2011 Vienna, workshop
Dear bioinfo-core community:
Thanks to your feedback, we have identified two broad session topics for the
workshop at ISMB 2011 in Vienna July 15 to 19th (roughly). Workshop
are due this Friday and we ask for your feedback on the topics and request
speaker proposals if you desire to present within one of the sessions.
provide proposals by Thursday to myself or one of the co-organizers (Fran
Lewitter, Simon Andrews or David Sexton).
Topic 1: Analysis Pipelines for NGS--the school of hard knocks.
A major goal of the bioinformatics core facility is to
high-quality data and tools to the researcher. In NGS workflows, core
facilities deliver both default data from analysis pipelines as well as
investigators to use those pipelines directly. However, there can be major
issues in doing so. This topic will explore the pitfalls by focusing on
information is missed by relying on standard pipelines only. How can one
actually get it wrong by delivering only the results of a standard pipeline?
What is the value of the intermediate data that you may not look at but if
do, there can be some rather interesting finds? Time and value can be in
conflict in these situations as in-depth QA/QC of data beyond standard
Topic2: Management of Core Facilities.
We will explore different business models of bioinformatics
facilites and their setup including business models, recharging, funding,
retention, and performance evaluations and metrics. This is a topic we have
discussed throughout the years, but continues to be of high interest.
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the
contains patient information, please contact the Partners Compliance
http://www.partners.org/complianceline . If the e-mail was sent to you in
but does not contain patient information, please contact the sender and
dispose of the e-mail.
bioinfo-core mailing list
The Galaxy Project is putting together a workshop proposal for ISMB/ECCB.
The theme of the proposed workshop will be "Genomics for Emerging Models" or
"Genomics: Flying without a reference". We want to have 4 talks that show
attendees particular solutions to challenges that arise when working with
organisms that don't have a closely related reference genome available. *The
proposal is due Friday, February 11*, in just two days.
Our aim is to highlight the solutions, with Galaxy gluing it all together,
but not being the focus of the workshop. We want to highlight the science
while also demonstrating the power of Galaxy.
If you have an approach that addresses a challenge with non-model organisms
(and that approach involves Galaxy!), please consider presenting it at ISMB
as part of this workshop proposal. *If we get more than 4 proposals, we'll
make a final call on what to include in the proposal on Thursday night. *
Workshop guidelines and info are at
Please let me know if you have any questions.