Hi guys,
I tried to use http://biocloudcentral.org/
But it said "Amazon connection problem: A problem starting EC2
instance. Check AWS console. " It did create a new keypair and
security group though.
Where does it want to look for additional information? Also Should I
maybe not being using this service yet? Is it still in beta?
Thanks again,
Greg
Hello again,
In the picture below, it seems like the prompt for Autoscaling is obscuring
the colour legend for the server status icons.
Is there any way to show the legend ?
Thanks.
[image: load.png]
--
Greg Edwards
gedwards2(a)gmail.com
Hi Everyone,
I'm trying to set up Cloud man.
I believe I followed the instructions listed here to a T:
http://wiki.g2.bx.psu.edu/Admin/Cloud
After launching the instance I even waited 20 minutes before trying to
access the public DNS
ec2-xxx-xx-xx-xx.compute-1.amazonaws.com/cloud, but my browser just says:
The connection has timed out
The server at ec2-xxx-xx-xx-xx.compute-1.amazonaws.com is taking too
long to respond.
Any ideas what I should check? I'm stuck. What information would be useful?
Info:
Zone is us-east-1a
Type is m1.large
root devide is ebs
AMI Name: galaxy-cloudman-2011-03-22
Region is US East (Virginia)
I used this format for user data:
cluster_name: <DESIRED CLUSTER NAME>
password: <DESIRED Galaxy CloudMan WEB UI PASSWORD>
access_key: <YOUR AWS ACCESS KEY>
secret_key: <YOUR AWS SECRET KEY>
However this screenshot shows a pipe delimited deal? Maybe I should try that?
http://userwww.service.emory.edu/~eafgan/content/galaxy_cloud/AWSconsole-4.…
Thanks,
Greg
Hi folks,
I've researched this in the new global Google Search tool
http://galaxy.psu.edu/search/web/ but didn't see the answer I needed.
Is there actually a single "version" of Galaxy ? or is it a collection of
components with their own versions ?
Can that can be seen on or near the Main front page ? I can't see a
Version/About type of item, either in menus or lurking in some rev stamp at
the bottom of pages etc.
Thanks.
--
Greg Edwards
gedwards2(a)gmail.com
Dear Galaxy Expert,
I would like to use Galaxy to de-novo assembly single-end read illumina
data (140bp) for plant transcriptomes (without reference). I remember
early emails mention trinity in Galaxy. But I could not see at Galaxy web
http://main.g2.bx.psu.edu/root
. Maybe it is installed in Amarzon EC2? Other suggestions in de-novo
assembly plant transcriptomes without reference.
Many thanks and look forward to hearing back from you,
Jane
<galaxy-user(a)bx.psu.edu>
Dear Galaxy Expert,
I would like to use Galaxy to de-novo assembly single-end read illumina
data (140bp) for plant transcriptomes (without reference). I remember
early emails mention trinity in Galaxy. But I could not see it at Galaxy
web http://main.g2.bx.psu.edu/root. Maybe it is installed in Amarzon EC2?
Other suggestions in de-novo assembly plant transcriptomes without
reference.
Many thanks and look forward to hearing back from you,
Baohua
<galaxy-user(a)bx.psu.edu>
Hi Antoine.
Thanks - sorry, I haven't analysed that particular platform - anyone?
http://picard.sourceforge.net/picard-metric-definitions.shtml#HsMetrics
seems comprehensive...
Why not try the Galaxy picard Hybrid Selection metrics tool on your data?
On Wed, Dec 21, 2011 at 6:25 PM, Antoine ROUSSELIN
<a.rousselin(a)baclesse.fr> wrote:
>
> Hello,
>
> My English is very bad, it's a shame!
>
> My I have a file for my baits (create a bed file of your Agilent SureSelect targets with exons and introns captured). Sequencing output, I get the files. Bam, my result sets of alignments on the human genome complete (with CASAVA). I try to get the coverage I only exonic regions (+ or - 50 bp).
>
> Thanks
>
> ROUSSELIN Antoine
> Clinical Biology and Oncology Laboratory
> Centre François BACLESSE
> France/Caen
> a.rousselin(a)baclesse.fr
> Tel : (33) 02.31.45.40.44
> Fax : (33) 02.31.45.50.53
>
>
>
> -------- Message d'origine--------
> De: Ross [mailto:ross.lazarus@gmail.com]
> Date: mer. 12/21/2011 03:16
> À: Antoine ROUSSELIN
> Cc: galaxy-user(a)lists.bx.psu.edu
> Objet : Re: [galaxy-user] % On-Off target
>
> Hello Antoine,
> I'm not sure I really understand your question but if the metrics described
> at http://picard.sourceforge.net/picard-metric-definitions.shtml#HsMetrics are
> of use, you could try the picard hybrid selection metrics Galaxy tool or
> use it on the command line. Otherwise perhaps you can get a more helpful
> response if you provide a clear explanation of the data formats you have
> and the measures you want.
>
>
> On Wed, Dec 21, 2011 at 2:59 AM, Antoine ROUSSELIN
> <a.rousselin(a)baclesse.fr>wrote:
>
> > **
> >
> > hello,
> > I'm looking for a tool (or command line) to determine the % On-Off target
> > + or - 50 bp of exon from my capture file but not annotated (!!!). Capture
> > SureSelect agilent home.
> >
> > Current pipeline:
> > GAIIx Illumina
> > CASAVA1.8
> > IGV
> > CNV-seq
> > SAMtools
> > BEDtools
> > GALAXY
> > NextGENe
> >
> > Please HELP
> >
> > ROUSSELIN Antoine
> > Clinical Biology and Oncology Laboratory
> > Centre François BACLESSE
> > France/Caen
> > a.rousselin(a)baclesse.fr
> > Tel : (33) 02.31.45.40.44
> > Fax : (33) 02.31.45.50.53
> >
> >
> > ___________________________________________________________
> > The Galaxy User list should be used for the discussion of
> > Galaxy analysis and other features on the public server
> > at usegalaxy.org. Please keep all replies on the list by
> > using "reply all" in your mail client. For discussion of
> > local Galaxy instances and the Galaxy source code, please
> > use the Galaxy Development list:
> >
> > http://lists.bx.psu.edu/listinfo/galaxy-dev
> >
> > To manage your subscriptions to this and other Galaxy lists,
> > please use the interface at:
> >
> > http://lists.bx.psu.edu/
> >
>
>
>
> --
> Ross Lazarus MBBS MPH;
> Associate Professor, Harvard Medical School;
> Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
>
--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
hello,
I'm looking for a tool (or command line) to determine the % On-Off target + or - 50 bp of exon from my capture file but not annotated (!!!). Capture SureSelect agilent home.
Current pipeline:
GAIIx Illumina
CASAVA1.8
IGV
CNV-seq
SAMtools
BEDtools
GALAXY
NextGENe
Please HELP
ROUSSELIN Antoine
Clinical Biology and Oncology Laboratory
Centre François BACLESSE
France/Caen
a.rousselin(a)baclesse.fr
Tel : (33) 02.31.45.40.44
Fax : (33) 02.31.45.50.53