The best way to move individual datasets b/t Galaxy instances is by link: right click on the dataset's save icon (a disk), copy the link, and paste that into the upload form.
A couple word of caution about our test server: it is experimental and may be nonfunctional or unavailable periodically, there is little/no support is offered for new tools, and quotas are quite low. For analyses that require multiple steps, test most likely will not meet your needs.
Finally, please always cc the mailing list when replying.
On Jan 9, 2012, at 7:48 PM, Wei Liao wrote:
> Hi, Jeremy,
> Thank you for your help，I will try to use pileup tool.
> I noticed that there are many great tools I am interested on the test server such as GATK, however, all my data are on main server and the bam files are huge (5-7GB), do you know a fast way to transfer data from main server account to test server?
> Wei It
> On Mon, Jan 9, 2012 at 10:40 AM, Jeremy Goecks <jeremy.goecks(a)emory.edu> wrote:
> The pileup tool will help you find SNPs in your data; you'll want to read the documentation to understand how best to use it for your needs. You can also try the Unified Genotyper on our test server ( http://test.g2.bx.psu.edu/ ), but it's in alpha/beta status and we aren't providing any support for it yet.
> Good luck,
> On Jan 9, 2012, at 1:28 AM, <ericliaowei(a)gmail.com> <ericliaowei(a)gmail.com> wrote:
>> I am new to the RNA-seq, and the only available sources for me to do analysis is the Galaxy server. I want find out SNP and point mutations in RNA-Seq data using Galaxy (I do not know if anyone using RNA-seq data to find point mutations, because there is whole Genome sequencing for reporting mutations and SNPs). I have been searching in the forum for a step-by-step protocols for doing it, but could not find it.
>> I have one normal sample and two cancer samples, a TopHat produced "accepted Hits.bam" file for each one.
>> I want to find out SNP and point mutations in the cancer samples, so How do I go from here? Can anyone show me how to do it in Galaxy main server?
>> The Galaxy User list should be used for the discussion of
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>> at usegalaxy.org. Please keep all replies on the list by
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> Wei Liao
> Research Scientist,
> Brentwood Biomedical Research Institute
> 16111 Plummer St.
> Bldg 7, Rm D-122
> Sepulveda, CA 91343
> 818-891-7711 ext 7645
I am new to the RNA-seq, and the only available sources for me to do analysis is the Galaxy server. I want find out SNP and point mutations in RNA-Seq data using Galaxy (I do not know if anyone using RNA-seq data to find point mutations, because there is whole Genome sequencing for reporting mutations and SNPs). I have been searching in the forum for a step-by-step protocols for doing it, but could not find it.
I have one normal sample and two cancer samples, a TopHat produced "accepted Hits.bam" file for each one.
I want to find out SNP and point mutations in the cancer samples, so How do I go from here? Can anyone show me how to do it in Galaxy main server?
I was wondering how the sharestring feature works?
Enis mention it a little bit here:
So as I understand it, I do my customizations and persist them, and
then I get a sharestring so others can load my customizations.
How does this work behind the scenes?
Also where are my customizations stored? Am I charged by Amazon for
storing them? How do others have permissions to pull them from my
(I'm new to all of this, sorry if my questions are obvious)
I could use some help on adding a tool to the cloud version of Galaxy. The
Cloud startup process creates, among other things,
/mnt/galaxyTools/galaxy-central which has tools_conf.xml, and subdir tools
etc. This seems not accessible before starting the cloud. I assume I need
to add my tool into the structure as per a local Galaxy instance, and then
get Galaxy to restart, or re-read it's config ? Would appreciate some
Just as background .. I have got a custom proteomics Perl script running ok
under a local version of Galaxy on Mac. Added in to tools_conf.xml, tools
etc. Made several mods to the Perl to stop any writing to stderr except for
fatal show-stopper errors, everyone seems to hit that one, and other small
things to make it play better with Galaxy. Also quite familiar with AWS
EC2, have been using that for a while.
I have Galaxy Cloudman running well, start/stop extra servers etc. Using
the free t1.micro AMI for now, slowish but ok for testing. Or a Spot
Instance of m1.large when I'm impatient.
I couldn't find the answer in a search of Galaxy archives, apologies if
it's there, or obvious in some other way.
Port Jackson Bioinformatics Consulting.
Would be grateful I the following genomes were uploaded into Galaxy
Streptomyces coelicolor A3(2) ; ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Streptomyces_coelicolor_A3_2__uid...
Propionibacterium acnes KPA171202 (pre-salt downshift); ftp://ftp.ncbi.nih.gov/genomes/Bacteria/Propionibacterium_acnes_KPA171202...
Thanks in advance,
Dr Kenneth McDowall * Astbury Centre for Structural Molecular Biology
Tel +44 (0) 113 343 3109 or Mob. 0783 793 5384 | Ext 33109 | k.j.mcdowall(a)leeds.ac.uk<mailto:firstname.lastname@example.org> | www.fbs.leeds.ac.uk
IMCB Director of Taught Programmes * Institute of Molecular and Cellular Biology
Faculty of Biological Sciences | University of Leeds | Manton Building Room 10.05 | Leeds LS2 9JT | UK
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Is there any plumbing in place for handling errors that occur in component
tools of workflows? I'm thinking about a case where you might want to
follow path 'A' if a tool succeeds, but path 'B' if there is some specific
kind of exception, and fail completely if any other error is thrown.
If this is in place, a pointer to the relevant docs would be awesome. I've
looked around and did not come up with anything.
I have two small RNA libraries that are biological replicates. I mapped
the reads onto the genome using Bowtie and displayed the BAM files as
two individual tracks on the UCSC genome browser. However, this is not
Ideally, I would like to color the reads from each library with a
different color, so that I could display them in the SAME track. Because
the two replicates are color labeled, I would be able to tell which
experiment a particular read comes from.
I have two BAM files from each library. All I need to do is to label
them with different colors, then merge them before displaying on genome
Does anyone know how to do this?
Thanks in advance for your help!
Dear Galaxy users,
I have installed a local Galaxy instance on a server and I use it to run certain genomic assembly workflows. Nevertheless with larger datasets completion may take up to one day. How can i make Galaxy to continue the operation even when i close the browser? Is that possible on a local instance or on the main server?