[ensembl-dev] [Dev] lavToAxt

[Andy Yates]

Hi Ambrose,

Where did you get the program from? As far as I am aware it is available from Jim Kent's CVS & is the only place you can get it from. This blog has some good information on how to build it (unfortunately the maintainer has taken the blog down so it's only available from Google's cached copy)

http://webcache.googleusercontent.com/search?q=cache:uo_37vXjNEwJ:charybdis.eeb.ucla.edu/brantswiki/published/InstallingBlat+jim+kent+cvs&cd=2&hl=en&ct=clnk&client=safari

Anyway the server is at :pserver:anonymous at genome-test.cse.ucsc.edu:/cbse and the password is genome. The source can be checked out using 

cvs co -kk -rbeta kent 

I would check that the beta release tag is still valid. Once you've complied the general utilities/libraries then the lavToAxt should be available from hg/mouseStuff/lavToExt

Andy


On 27 Jul 2010, at 17:37, ambrose andongabo (RRes-Roth) wrote:

> Dear all ,
>                 I downloaded lav2axt because I could not find lavToAxt.  The parameter list for the lav2axt I downloaded is as follows
>  
> lav2axt: usage: lav-file human-genomic-seq [N=region-name] [D=cdb-directory] [F=fasta-directory]
>  
> and that of lavToAxt used in ensembl-compara  is as follows
>  
> system($self->lavToAxt, $lav_file, $query_nib_dir, $target_nib_dir, $axt_file)
>  
> The problem I have is that I get an error while running  chain-net. I will be please if somebody can tell me where I can get the executable for lavToAxt .
>  
> Many thanks in advance
>  
> thanks
>  
> Ambrose
>  
>  
>  
>  
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-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/