[Gmod-help] GMOD for Next Generation Sequencing

[Scott Cain]

Hi Bala,

I use exactly the commands on http://gmod.org/wiki/CVS_Access,
however, I imagine cvs is still not built in to Vista, so you'll need
another application to do the cvs checkout for you.  If eclipse isn't
working for you, you could try WinCVS:

  http://www.wincvs.org/download.html

I've used it occasionally on WinXP on the commandline and using the
same commands as in the CVS_Access page.  The names of the cvs
directories/repositories you need are Generic-Genome-Browser (but
don't provide a branch name like 'stable'; GBrowse 2 is the
main/default developement branch) and gbrowse-adaptors.

Please direct further questions about GBrowse to the GBrowse mailing list at:

  https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse

Thanks,
Scott


On Mon, Jun 1, 2009 at 2:26 PM, Selvaraj, Balamuruganand (B)
<BSelvaraj at dow.com> wrote:
>
> Scott,
>
> I tried the options provided in the link. But I get a connection timed out.
>
> Can you let me know, how are you trying to get the codes from CVS.
> May be I can try that option.
>
> All I need is the Gmod-Adaptor directory and 'Gbrowse 2' from the CVS.
>
> Best regards,
> Bala
>
> -----Original Message-----
> From: Scott Cain [mailto:scott at scottcain.net]
> Sent: Monday, June 01, 2009 12:30 PM
> To: Selvaraj, Balamuruganand (B)
> Cc: help at gmod.org
> Subject: Re: [Gmod-help] GMOD for Next Generation Sequencing
>
> Hi Bala,
>
> I don't know anything about using eclipse for getting cvs checkouts,
> but this page:
>
>  http://lampsig.org/new/archives/17-LAMPSig-Class-2.0-Using-Eclipse-to-get-a-CVS-Project.html
>
> has a description for how to do it as a developer, and one of the
> commentors describes how to do it anonymously.
>
> Does that help?
>
> Scott
>
>
> On Mon, Jun 1, 2009 at 10:41 AM, Selvaraj, Balamuruganand (B)
> <BSelvaraj at dow.com> wrote:
>>
>> Dave,
>>
>> Can you also let me know how we can connect to Gbrowse CVS.
>> Although, I have all info (from Wiki)reg the CVS, I get error while I
>> try to add cvs host server as "gmod.cvs.sourceforge.net".
>>
>> Kindly let me know the following info.
>> Host:
>> Repository Path:
>>
>> Kindly confirm, if the following information is correct
>> User:login
>> Password:\n
>>
>> I am using windows platform and eclipse for getting the source code from
>> CVS.
>>
>> Thanks in advance for your reply.
>>
>> Best regards,
>> Bala
>>
>> -----Original Message-----
>> From: Selvaraj, Balamuruganand (B)
>> Sent: Monday, June 01, 2009 8:04 AM
>> To: 'help at gmod.org'
>> Subject: RE: [Gmod-help] GMOD for Next Generation Sequencing
>>
>>
>> Hi Dave,
>>
>> Thanks for your reply.
>> Since, I am relatively new to Gbrowse, I am still figuring out many
>> things.
>>
>> It will be really great if you could pass on some documentation
>> regarding the SAMtools adaptor.
>> I had another small question. Are there any utilities which convert the
>> sequence files from Solexa sequencing machines to SAM format.
>>
>> Thanks again !
>>
>> Best regards,
>> Bala
>>
>> -----Original Message-----
>> From: Dave Clements, GMOD Help Desk [mailto:gmodhelp at googlemail.com]
>> Sent: Friday, May 29, 2009 5:16 PM
>> To: Selvaraj, Balamuruganand (B)
>> Cc: GMOD Help Desk
>> Subject: Re: [Gmod-help] GMOD for Next Generation Sequencing
>>
>> Hi Bala,
>>
>> Yes, although the presentation you are looking at did not use it
>> because it didn't yet exist.
>>
>> In the last few months Lincoln has written a SAMtools database adaptor
>> for GBrowse.  It's available in CVS in GBrowse under the
>> gbrowse-adaptors directory.  I just got it really working on my laptop
>> today.
>>
>> SAMtools is a set of programs that manipulate files in SAM and BAM
>> format.  BAM is the binary version of SAM.  SAM is an indexed,
>> compressed short read format.  The GBrowse adaptor reads from it.
>>
>> However, some big caveats:
>> 1. It is only useful in GBrowse 2.  In GBrowse 1 you can only specify
>> one adaptor.  Not so in 2.
>> 2. It is not currently documented.
>>
>> I'm giving two talks on this in the next two weeks.  The first talk
>> should be available on the GMOD web site around June 7.   A wiki
>> version of that talk should be available on the GMOD web site by the
>> end of June.
>>
>> Is that soon enough?  If not I can go through my notes and try and
>> extract something meaningful.
>>
>> Also note that the SAMtools adaptor only changes the E coli part of
>> that presentation.  Everything shown in the threespine stickleback is
>> still done using long existing technology (and lots of disk space).
>>
>> Dave C.
>>
>> On Fri, May 29, 2009 at 1:58 PM, Selvaraj, Balamuruganand (B)
>> <BSelvaraj at dow.com> wrote:
>>>
>>> Hi Dave Clement,
>>>
>>> I am currently trying to use Gbrowse for view Next generation
>> Sequencing
>>> alignments.
>>> I just saw slides of the GMOD's NGS workshop in Germany
>>> (http://gmod.org/wiki/Image:NGSWithGMODWorkshop.pdf)
>>>
>>> I wanted to know if the plugins for GMOD have already been developed.
>>>
>>> Thanks for your reply.
>>>
>>> Best regards,
>>> Bala
>>
>>
>>
>> --
>> Was this helpful?  Let us know at
>> http://gmod.org/wiki/Help_Desk_Feedback
>>
>> Learn more about GMOD at:
>>  SMBE:
>> http://ccg.biology.uiowa.edu/smbe/symposia.php?action=view&sym_ID=27
>>  Arthropod Genomics: http://www.k-state.edu/agc/symp2009/seminar.html
>>  AGA Next Gen Seq in Non-Models:
>> http://www.regonline.com/Nextgeneration
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research