Bug ? in Galaxy Cloudman display
by Greg Edwards
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
9 years, 9 months
How to determine version of Galaxy from main page
by Greg Edwards
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
9 years, 9 months
suggestions for de novo assembly plant transcriptome without reference
by Jane Song
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>
9 years, 9 months
De novo assembly plant transcriptome
by Bao-Hua Song
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>
9 years, 9 months
Re: [galaxy-user] RE : % On-Off target
by Ross
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;
9 years, 9 months
% On-Off target
by Antoine ROUSSELIN
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
9 years, 9 months
Search the Galaxy!
by Dave Clements
Hello all,
I am happy to announce that Galaxy now has several Google Custom Searches
that make it much easier (really - way, way easier) to find answers to your
questions about Galaxy. They are available at
http://galaxyproject.org/search/.
*Name & URL *
* Description *
**
*Galaxy Web Search <http://galaxyproject.org/search/web>*
http://galaxyproject.org/search/web
Searches *everything:* Galaxy Main <http://wiki.g2.bx.psu.edu/Main>,
the mailing
list archives <http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>, the Galaxy
wiki <http://wiki.g2.bx.psu.edu/FrontPage>, Galaxy's source code at
Bitbucket <https://bitbucket.org/galaxy/galaxy-central/src/tip/>, and the Tool
Shed <http://wiki.g2.bx.psu.edu/Tool%20Shed>. The results are returned in a
unified list, and are also grouped into several categories.
*Galaxy Mailing List Search <http://galaxyproject.org/search/mailinglists>*
http://galaxyproject.org/search/mailinglists
Searches all the Galaxy mailing list
archives<http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>.
The results are returned in a unified list, and are also grouped by mailing
list.**
*UseGalaxy Search <http://galaxyproject.org/search/usegalaxy>*
http://galaxyproject.org/search/usegalaxy
Search for information about *using* Galaxy. Searches Galaxy
Main<http://wiki.g2.bx.psu.edu/Main>(
UseGalaxy.org <http://usegalaxy.org/>), the
wiki<http://wiki.g2.bx.psu.edu/Learn>(excluding the
Admin <http://wiki.g2.bx.psu.edu/Admin> pages), and the Galaxy-User and
Galaxy-Announce mailing list
archives<http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>.
*GetGalaxy Search <http://galaxyproject.org/search/getgalaxy>*
http://galaxyproject.org/search/getgalaxy
Search for information about installing, customizing, and developing
Galaxy. Searches the Galaxy Bitbucket (source)
site<https://bitbucket.org/galaxy/galaxy-central/src/tip/>,
the Tool Shed <http://toolshed.g2.bx.psu.edu/>, the
wiki<http://wiki.g2.bx.psu.edu/Admin>(excluding the
Learn <http://wiki.g2.bx.psu.edu/Learn> pages), and the Galaxy-Dev and
Galaxy-Announce mailing list
archives<http://wiki.g2.bx.psu.edu/Mailing%20Lists#Searching>.
We strongly encourage you to give these try. Please send feedback and
suggestions to Galaxy Outreach <outreach(a)galaxyproject.org>.
Happy searching (and a Happy New Year!),
Dave Clements
--
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://galaxyproject.org/wiki/
9 years, 9 months
