[galaxy-user] Cufflink error

[Lizex Husselmann]

Hi 

I've started an alignment using the command line (Tophat v1.3.3). I've uploaded 
the files (accepted.bam) onto Galaxy and upon doing the Cufflinks analysis on 
the Galaxy interface, it shows an error. I had to look at the options. I've 
change the options to default and run it again but still the same error. Is the 
accepted.bam file not compatible with the Galaxy Cufflinks? Is there something 
I not doing? 

Kind regards 

Lizex 
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Re: [galaxy-user] question about uploading data through URL method

[Xiangming Ding]

Hi
 the file name is spr097786.fastq.bz2.After upload it showed  
spr097786.fastq. It showed it only contain around 5000 sequence reads.
 I also tried to upload through FTP. so i download the file to my  
computer and then upload to FTP in galaxy.  the totlal 800M file was  
uploaded to the FTP successfully. But when i transfered the file to  
the history i met the same problem. only 5000 sequence reads was moved  
to history. I donnot whether it is because of the bz2 file extension.  
or i should try other compressed file extension.


xaingmimg

Quoting Jennifer Jackson :


Hello Xiangmimg,

Data files can be loaded using a URL on the "Get Data => Upload"  
form. FTP and HTTP connections are supported. This is briefly  
described on that form.


If you are still having issues, there may be a problem with file  
compression or the connection. Downloading locally then using  
Galaxy's FTP upload function is certainly an option.

http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP

Best,

Jen
Galaxy team

On 11/6/11 8:54 PM, Xiangming Ding wrote:

Hi galaxy

I am a new user of galaxy. i met a problem and didnot find similar
question in FAQ. I wanted to upload the data from DDBJ DRA dataset to
galaxy through UTL method. The file is around 800M. However after
uploading, the FASTQ file was just around 2M. So I wanted know whether
it is possible to upload a large file to galaxy through URL method? or I
should download the file to my pc and then uploading to galaxy through
FTP method.

Thanks

xiangmimg
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http://galaxyproject.org/wiki/Support




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[galaxy-user] Cuffcompare error

[Alessia D]

Hi,

I am trying to run Cuffcompare on a set of 6 Cufflinks-generated datasets
(3 replicates of 2 conditions).  I am consistently getting the following
error:

Error running cuffcompare. Warning: Your version of Cufflinks is not
up-to-date. It is recommended that you upgrade to Cufflinks v1.1.0 to
benefit from the most recent features and bug fixes
(http://cufflinks.cbcb.umd.edu).
Error: no XLocus created for transcript CUFF.34072.1 (file ./input3)
[2, 2], on chrY+:274296-277218


However, if I run Cuffcompare on the 2 conditions separately (3x Cufflinks
datasets), everything works fine.
Does anyone know why this is?

Thanks

Alessia
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Re: [galaxy-user] Data gets deleted from public server

[shamsher jagat]

Yes I was and infect when I logged out and logged in back it was there then
I left for lunch and when I come back data is not there? It is weird.
Shamsher


On Mon, Nov 7, 2011 at 5:00 PM, Nate Coraor  wrote:

> On Nov 7, 2011, at 7:11 PM, shamsher jagat wrote:
>
> > I uploaded two BAM files and was working with them but when I tried to
> use them again they are automatically deleted along with all the steps of
> analysis?
> > Any reason or I am missing something.
>
> Hi Shamsher,
>
> Were you logged in when you performed this analysis?
>
> --nate
>
> >
> > Shamsher
> > ___
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>
>
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Re: [galaxy-user] Data gets deleted from public server

[Nate Coraor]

On Nov 7, 2011, at 7:11 PM, shamsher jagat wrote:

> I uploaded two BAM files and was working with them but when I tried to use 
> them again they are automatically deleted along with all the steps of 
> analysis?
> Any reason or I am missing something.

Hi Shamsher,

Were you logged in when you performed this analysis?

--nate

> 
> Shamsher
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> 
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[galaxy-user] Data gets deleted from public server

[shamsher jagat]

I uploaded two BAM files and was working with them but when I tried to use
them again they are automatically deleted along with all the steps
of analysis?
Any reason or I am missing something.

Shamsher
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Re: [galaxy-user] downloading (and renaming) output files from Galaxy public server

[Jennifer Jackson]

Hi Rich,

This is a good question! Maybe people have been asking about this. To 
download data with a unix line command method, please try wget or curl, 
for example:


unix% wget 'url_for_the_dataset'

or

unix% wget 'url_for_the_history'

To capture the url for a dataset, right click on the disk icon for a 
dataset and select "copy link location".


To capture the url for an entire history, select "Options -> Export to 
File". The middle panel will display a link.


A downloaded history can be loaded into a local Galaxy instance where 
the datasets can be managed (copy/rename) or the histories archived.


Hopefully this helps you and others that are managing larger datasets & 
histories,


Best,

Jen
Galaxy team


On 11/7/11 7:50 AM, Richard Mark White wrote:

Hi,
I am using the galaxy public server.
Is there a way to access output files (via ftp, perhaps) so I can bulk
download them to my computer? I am over my quota and want to get data
off of Galaxy but prefer not to do this all one at a time.
Similarly, is there a way to access a directory (via unix, ftp, etc) to
rename files quickly while they are on Galaxy, since renaming each
output file (i.e. the multiple ones output from cuffdiff) within galaxy
is very inefficient and time consuming.

Thanks.

Rich




--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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[galaxy-user] downloading (and renaming) output files from Galaxy public server

[Richard Mark White]

Hi,
 I am using the galaxy public server.
 Is there a way to access output files (via ftp, perhaps) so I can bulk 
download them to my computer? I am over my quota and want to get data off of 
Galaxy but prefer not to do this all one at a time.  
 Similarly, is there a way to access a directory (via unix, ftp, etc) to rename 
files quickly while they are on Galaxy, since renaming each output file (i.e. 
the multiple ones output from cuffdiff) within galaxy is very inefficient and 
time consuming.

Thanks.

Rich___
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Re: [galaxy-user] question about uploading data through URL method

[Jennifer Jackson]

Hello Xiangmimg,

Data files can be loaded using a URL on the "Get Data => Upload" form. 
FTP and HTTP connections are supported. This is briefly described on 
that form.


If you are still having issues, there may be a problem with file 
compression or the connection. Downloading locally then using Galaxy's 
FTP upload function is certainly an option.

http://wiki.g2.bx.psu.edu/Learn/Upload%20via%20FTP

Best,

Jen
Galaxy team

On 11/6/11 8:54 PM, Xiangming Ding wrote:

Hi galaxy

I am a new user of galaxy. i met a problem and didnot find similar
question in FAQ. I wanted to upload the data from DDBJ DRA dataset to
galaxy through UTL method. The file is around 800M. However after
uploading, the FASTQ file was just around 2M. So I wanted know whether
it is possible to upload a large file to galaxy through URL method? or I
should download the file to my pc and then uploading to galaxy through
FTP method.

Thanks

xiangmimg
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The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
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please use the interface at:

http://lists.bx.psu.edu/


--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/Support
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Re: [galaxy-user] question about uploading data through URL method

[Simao Lee]

You can download DRA files directly by FTP to Galaxy . .
Just paste the FTP address directly in the file box when using upload from
my computer
Best

Simon

On 7 November 2011 04:54, Xiangming Ding  wrote:

> Hi galaxy
>
> I am a new user of galaxy. i met a problem and didnot find similar
> question in FAQ. I wanted to upload the data from DDBJ DRA dataset to
> galaxy through UTL method. The file is around 800M. However after
> uploading, the FASTQ file was just around 2M. So I wanted know whether it
> is possible to upload a large file to galaxy through URL method? or I
> should download the file to my pc and then uploading to galaxy through FTP
> method.
>
>  Thanks
>
> xiangmimg
> __**_
> 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/
>
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