Hi, Jorge,
Galaxy source includes the Galaxy interfaces but not the third party
executables for tools like fastqc or bwa. They can be automagically
installed if you install the tool from a tool shed but at a guess, you are
working on your desktop with the fastqc tool in a recent clone of galaxy?
Un
Hi, Yan
The htseq_bams_to_count_matrix tool in the test toolshed might be worth a
try - it creates tabular count matrices from any number of individual
sample bam/sam files (it is NOT read group aware!). Each row contains the
count for that contig for each sample. It uses HTSeq code and you supply
Hi, Lahcen.
http://wiki.galaxyproject.org/Admin/Config/Performance/ProductionServer#Use_a_clean_environmentwill
probably help fix this for you.
On Mon, Aug 5, 2013 at 9:44 PM, lahcen campbell wrote:
> Hi,
>
> I am trying to install a local version of galaxy on my mac book (x86_64,
> OSx 10.8.4).
e
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Hi, Thanh,
If your primary goal is inference about differential 'gene' expression
taking biological variability into account with biological replicates for
each of two conditions, you might want (eg see Dillies et al.,
http://bib.oxfordjournals.org/content/early/2012/09/15/bib.bbs046.long and
http:
lib/galaxy/datatypes/genetics and the
tools that use it (eg TDT or CaCo tools) in tools/rgenetics for more
complex hackery keeping related files needed by plink together.
On Fri, Jan 4, 2013 at 9:50 AM, wrote:
> Thanks for the help Ross.
>
> ** **
>
> Any chance you can poi
some relevant Galaxy
composite datatype experience. There is some documentation but it's not
extensive or transparent.
Good luck.
On Fri, Jan 4, 2013 at 9:19 AM, wrote:
> Hi Ross,
>
> I don’t know of any tools that work in the way I want, but
> I’m not an
used in some rgenetics tools) but arbitrary data structures are not going
to be possible AFAIK. You're unlikely to get useful help without a much
more complete and clear explanation of the problem.
On Thu, Jan 3, 2013 at 1:50 PM, wrote:
> Hi Ross,
> I think I need to c
Try importing those library files to the history where you want them -
browse the Galaxy 'shared data' tab to where you uploaded them.
On Wed, Jan 2, 2013 at 11:39 AM, wrote:
> Hi,
>I have a local galaxy installation.
>
> I've created a data library, selected "Upload files from filesystem
>
gt;
> http://lists.bx.psu.edu/listinfo/galaxy-dev
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--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://schol
Neil, have you tried the 'impersonate user' option in the security
group on the admin menu?
AFAIK it works for local authentication but not for external
authentication setups...
On Thu, Oct 25, 2012 at 1:02 PM, wrote:
> Hi,
>
> We have a local instance of Galaxy installed. If a user logs in
erver
> 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
&g
On Wed, Oct 3, 2012 at 9:11 PM, i b wrote:
> Dear all,
> how reliable is running Cuffdiff without replicates? e.g.one samples
> agains another one?
>
> Is it statistically makign any difference when using replicates?
Seqanswers might be a better place to ask this very interesting
technical questi
in your mail client. For discussion of
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ion of
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> 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:
Hi, Carly.
Hover your mouse pointer over the little floppy disk icon and the help
text 'download' should appear - click the icon to download the
contents of the file to your local workstation. It's an interval file
so it will be tab delimited and should open easily in your favourite
spreadsheet pr
using "reply all" in your mail client. For discussion of
> local Galaxy instances and the Galaxy source code, please
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> pl
;> >
>> > --
>> > Greg Edwards,
>> > Port Jackson Bioinformatics
>> > gedwar...@gmail.com
>> >
>> > ___
>> > The Galaxy User list should be used for the discussion of
>> >
31.45.40.44
> Fax : (33) 02.31.45.50.53
>
>
>
> Message d'origine
> De: Ross [mailto:ross.laza...@gmail.com]
> Date: mer. 12/21/2011 03:16
> À: Antoine ROUSSELIN
> Cc: galaxy-user@lists.bx.psu.edu
> Objet : Re: [galaxy-user] % On-Off target
>
&g
opment list:
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--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medi
ur subscriptions to this and other Galaxy lists,
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--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
___
y source code, please
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>
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>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
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--
Ross Lazarus MBBS MPH;
Associate
p://lists.bx.psu.edu/listinfo/galaxy-dev
>
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> please use the interface at:
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--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Head, Medical Bioinformatics, Ba
ut the bug.
On Thu, Aug 4, 2011 at 12:02 PM, Ross wrote:
> Hi, Camille,
>
> I can see this really needs a 'proper' fix - preferably taking
> advantage of the automated header merge.
> Preserving the metadata from each bam automatically is safer and less
> error-prone but y
not wanted.
I'll let you know when you can try it out on our test instance and
which revision of the galaxy-central repository contains the changes
so you can get it working on your local installation.
On Wed, Aug 3, 2011 at 11:49 PM, Camille Stephan
wrote:
> Hi Ross,
> thanks for your
ep all replies on the list by
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AFAIK, the requirements stuff is still work in progress?
Yes, of course you're right - there has to be a better way -
particularly where there are complex inter-dependencies like
weblogo/python/corebio
On Thu, Jul 7, 2011 at 10:41 PM, Holger Klein wrote:
> Hi Ross,
>
> On 07/07
ht path to that weblogo script (marked executable)?
Can the user each job runs as execute it?
On Thu, Jul 7, 2011 at 7:56 PM, Holger Klein wrote:
> Hi Ross,
>
> On 07/07/2011 02:07 AM, Ross wrote:
>
>> Please try the new version 0.4 of the weblogo wrapper in
>> galaxy-cent
Hi Ross,
>
> thanks for taking care of this issue.
>
> On 07/05/2011 12:31 AM, Ross wrote:
>
>> Is this error seen on Galaxy main or test? If so please share the
>> history with me so I can see the input and reproduce what sounds like
>> a wrapper error?
>>
>
ts.bx.psu.edu/listinfo/galaxy-dev
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>
--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +
tances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
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> please use the interface at:
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--
Ross Lazarus
es and the Galaxy source code, please
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>
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> please use the interface at:
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>
--
Ross Laza
On Thu, Jun 9, 2011 at 10:12 AM, John David Osborne wrote:
> Thanks Ross, I don't see it under my local install - are there any
> pre-written scripts to integrate it with a local galaxy instance?
>
> I assume you are talking about this tool here:
> http://www.bioinformatics.
your subscriptions to this and other Galaxy lists,
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--
Ross Lazarus MBBS MPH;
Associate Professor, Harvard Medical School;
Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850;
Head, Medical Bioinformatics, BakerID
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:
>
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source code, please
> use the Galaxy Development list:
>
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--
Ross Lazarus MBBS MPH
Associate Pr
e first time some tools are run on a new dataset. There
are built in converters (use the pencil icon) also if you need them.
I hope this helps - thanks for using Galaxy and Rgenetics - please let
us know how you go and feel free to contact me if you have other
questions.
On Fri, Feb 18, 2011 at 9:
st regards,
> Sylvain
>
>
>
>
>
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>
--
Ross Lazarus MBBS MPH
Associate Professor, HMS; Director of Bioinformatics,
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