[ensembl-dev] [Dev] lavToAxt

[Maximilian Haussler]

Hi Andy and Ambrose,

Please note that UCSC is changing to git as a version control system and
they are using an external PNG library now.

the basic compilation from the most current zipfile is described here and
has not changed:
genome.ucsc.edu/admin/jk-install.html

You can also check out source code from git
(genome.ucsc.edu/admin/git.html) but
I recommend sticking to the zipfile for a start .

<http://genome.ucsc.edu/admin/jk-install.html>Most older OS-specific
instructions will have to be adapted (e.g.
genomewiki.ucsc.edu/index.php/Source_tree_compilation_on_Debian/Ubuntu or
bergmanlab.smith.man.ac.uk/?p=32 for OSX).

Here are the latest download instructions / locations:
https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-July/002008.html

If you have further questions, don't hesitate to email them to
genome at soe.ucsc.edu

<https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-July/002008.html>
cheers
Max




On Wed, Jul 28, 2010 at 10:40 AM, Andy Yates <ayates at ebi.ac.uk> wrote:

> 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_37vXjOu NEwJ:charybdis.eeb.ucla.edu/brantswiki/published/InstallingBlat+jim+kent+cvs&cd=2&hl=en&ct=clnk&client=safari<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
> >
> >
> >
> >
> > _______________________________________________
> > Dev mailing list
> > Dev at ensembl.org
> > http://lists.ensembl.org/mailman/listinfo/dev
>
> --
> 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/
>
>
>
>
>
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>
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