Re: [galaxy-user] Large local file of NGS for FASTAQ Groomer

2012-02-13 Thread Arthur Zheng 
Dear Alex,

Thank you for the reminder.
I noticed that I am using illumina CASAVA 1.8.
How can I make sure whether it is already in Sanger format or not?

Arthur

On Mon, Feb 13, 2012 at 4:53 AM, Bossers, Alex  wrote:

> Are you sure the fastq's are in older format? Otherwise you won't need to
> groom the files anymore (as far as I understood) since the newer format is
> comparable Sanger quality score already Saves huge resources!
> Alex
>
>
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[galaxy-user] 2012 Galaxy Community Conference (GCC2012): Now Accepting Abstracts

2012-02-13 Thread Dave Clements 
Hello all,

Abstracts  are now
being accepted for oral presentations at the 2012 Galaxy Community
Conference (GCC2012) .
Submissions on any topics of interest to the Galaxy community are
encouraged. Areas of interest include, but are not limited to:

   - Best practices for local Galaxy installation and management
   - Integrating tools and/or data sources into the Galaxy framework
   - Deploying galaxy on different infrastructures
   - Compelling or novel uses of Galaxy for biomedical analysis

See the GCC2011 program  for an
idea of the breadth of topics that can be covered. Oral presentations will
be approximately 15-20 minutes long, including time for question and
answer. There will also be an opportunity for lightning talks, which will
be solicited at the meeting. The submission deadline is April 16. See
the GCC2012
Abstracts  page for
more details and how to submit.

GCC2012  will be held, July 25-27
in Chicago, Illinois, United States. The main meeting will run for two full
days , and be preceded by
a full day of training
workshops.
If you are a bioinformatics tool developer, data provider, workflow
developer, power bioinformatics user, sequencing or bioinformatics core
staff, or a data and analysis archival specialist, then GCC2012 is relevant
to you. Registration will open in March.
GCC2012 is hosted by the University of Illinois at Chicago ,
the University of Illinois at Urbana-Champaign , and
the Computation Institute .

Links:
http://galaxyproject.org/GCC2012
http://galaxyproject.org/wiki/Events/GCC2012/Abstracts

Thanks,

Dave Clements
-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
http://galaxyproject.org/wiki/
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[galaxy-user] Result of annotation hg18 and hg19 on one file

2012-02-13 Thread La Chi 
Hi everyone,
how can i write the result of both functions in one single file then history 
panel will show its result..
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Re: [galaxy-user] Large local file of NGS for FASTAQ Groomer

2012-02-13 Thread Bossers, Alex 
Are you sure the fastq's are in older format? Otherwise you won't need to groom 
the files anymore (as far as I understood) since the newer format is comparable 
Sanger quality score already Saves huge resources!
Alex

-Oorspronkelijk bericht-
Van: galaxy-user-boun...@lists.bx.psu.edu 
[mailto:galaxy-user-boun...@lists.bx.psu.edu] Namens Peter Cock
Verzonden: maandag 13 februari 2012 11:04
Aan: Arthur Zheng
CC: galaxy-user@lists.bx.psu.edu
Onderwerp: Re: [galaxy-user] Large local file of NGS for FASTAQ Groomer

On Mon, Feb 13, 2012 at 2:17 AM, Arthur Zheng  wrote:
>
> On Sun, Feb 12, 2012 at 4:34 PM, Peter Cock  wrote:
>>
>> On Sun, Feb 12, 2012 at 10:28 PM, Arthur Zheng  wrote:
>> > Hi,
>> >
>> > I have downloaded and installed a local instance of galaxy on the 
>> > linux server using my user account according to here:
>> > http://main.g2.bx.psu.edu/
>> >
>> > Then I ran the following command:
>> >> sh run.sh
>> > and accessed galaxy through the local firefox browser on the server
>> > http://localhost:8080
>> >
>> > Now I am trying to use some NGS files for FASTQ Groomer. Each file 
>> > is in the server disk already, but very large (~8G each).
>> > I was not able to use the "upload file from your computer" function 
>> > under the "Get Data" tab (maybe because each file is too large).
>> >
>> > What am I supposed to do?
>> >
>> > Thank you!
>> >
>> > Arthur
>>
>> The method you tried "uploads" the file from your computer back to 
>> itself - making a copy as it goes with lots of overhead. You should 
>> probably consider the procedure here which allows you to avoid even 
>> making a copy on disk but point at the existing files already on the 
>> server:
>>
>> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%
>> 20Files
>>
>> Peter
>
> Hi Peter,
>
> I have followed the link you provided and selected the option "Upload 
> directory of files".
> Now my NGS data are in the library, and I am wondering how I can feed them to 
> FASTQ Groomer?
>
> Thanks!
>
>
> Arthur

You must add library files to your current history via the "Shared Data"
menu at the top of the Galaxy window.

Peter
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Re: [galaxy-user] Large local file of NGS for FASTAQ Groomer

2012-02-13 Thread Peter Cock 
On Mon, Feb 13, 2012 at 2:17 AM, Arthur Zheng  wrote:
>
> On Sun, Feb 12, 2012 at 4:34 PM, Peter Cock  wrote:
>>
>> On Sun, Feb 12, 2012 at 10:28 PM, Arthur Zheng  wrote:
>> > Hi,
>> >
>> > I have downloaded and installed a local instance of galaxy on the linux
>> > server using my user account according to here:
>> > http://main.g2.bx.psu.edu/
>> >
>> > Then I ran the following command:
>> >> sh run.sh
>> > and accessed galaxy through the local firefox browser on the server
>> > http://localhost:8080
>> >
>> > Now I am trying to use some NGS files for FASTQ Groomer. Each file is in 
>> > the
>> > server disk already, but very large (~8G each).
>> > I was not able to use the "upload file from your computer" function under
>> > the "Get Data" tab (maybe because each file is too large).
>> >
>> > What am I supposed to do?
>> >
>> > Thank you!
>> >
>> > Arthur
>>
>> The method you tried "uploads" the file from your computer back to
>> itself - making a copy as it goes with lots of overhead. You should
>> probably consider the procedure here which allows you to avoid
>> even making a copy on disk but point at the existing files already
>> on the server:
>>
>> http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files
>>
>> Peter
>
> Hi Peter,
>
> I have followed the link you provided and selected the option "Upload 
> directory of files".
> Now my NGS data are in the library, and I am wondering how I can feed them to 
> FASTQ Groomer?
>
> Thanks!
>
>
> Arthur

You must add library files to your current history via the "Shared Data"
menu at the top of the Galaxy window.

Peter
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