<div>Hi Andy and Ambrose,</div><div><br></div>Please note that UCSC is changing to git as a version control system and they are using an external PNG library now.<div><br></div><div>the basic compilation from the most current zipfile is described here and has not changed:</div>
<div><a href="http://genome.ucsc.edu/admin/jk-install.html">genome.ucsc.edu/admin/jk-install.html</a></div><div><br></div><div>You can also check out source code from git (<a href="http://genome.ucsc.edu/admin/git.html">genome.ucsc.edu/admin/git.html</a>) but I recommend sticking to the zipfile for a start .</div>
<meta http-equiv="content-type" content="text/html; charset=utf-8"><meta http-equiv="content-type" content="text/html; charset=utf-8"><div><br></div><div><a href="http://genome.ucsc.edu/admin/jk-install.html"></a>Most older OS-specific instructions will have to be adapted (e.g. <a href="http://genomewiki.ucsc.edu/index.php/Source_tree_compilation_on_Debian/Ubuntu">genomewiki.ucsc.edu/index.php/Source_tree_compilation_on_Debian/Ubuntu</a> or <a href="http://bergmanlab.smith.man.ac.uk/?p=32">bergmanlab.smith.man.ac.uk/?p=32</a> for OSX).</div>
<div><br></div><div>Here are the latest download instructions / locations:</div><div><a href="https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-July/002008.html">https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-July/002008.html</a></div>
<div><br></div><div>If you have further questions, don't hesitate to email them to <a href="mailto:genome@soe.ucsc.edu">genome@soe.ucsc.edu</a></div><div><br></div><div><a href="https://lists.soe.ucsc.edu/pipermail/genome-mirror/2010-July/002008.html"></a>cheers</div>
<div>Max<br clear="all"><br></div><div><br>
<br><br><div class="gmail_quote">On Wed, Jul 28, 2010 at 10:40 AM, Andy Yates <span dir="ltr"><<a href="mailto:ayates@ebi.ac.uk">ayates@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi Ambrose,<br>
<br>
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)<br>
<br>
<a href="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" target="_blank">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</a><br>
<br>
Anyway the server is at :pserver:anonymous@genome-test.cse.ucsc.edu:/cbse and the password is genome. The source can be checked out using<br>
<br>
cvs co -kk -rbeta kent<br>
<br>
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<br>
<br>
Andy<br>
<div><div></div><div class="h5"><br>
<br>
On 27 Jul 2010, at 17:37, ambrose andongabo (RRes-Roth) wrote:<br>
<br>
> Dear all ,<br>
> I downloaded lav2axt because I could not find lavToAxt. The parameter list for the lav2axt I downloaded is as follows<br>
><br>
> lav2axt: usage: lav-file human-genomic-seq [N=region-name] [D=cdb-directory] [F=fasta-directory]<br>
><br>
> and that of lavToAxt used in ensembl-compara is as follows<br>
><br>
> system($self->lavToAxt, $lav_file, $query_nib_dir, $target_nib_dir, $axt_file)<br>
><br>
> 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 .<br>
><br>
> Many thanks in advance<br>
><br>
> thanks<br>
><br>
> Ambrose<br>
><br>
><br>
><br>
><br>
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<br>
--<br>
Andrew Yates Ensembl Genomes Engineer<br>
EMBL-EBI Tel: +44-(0)1223-492538<br>
Wellcome Trust Genome Campus Fax: +44-(0)1223-494468<br>
Cambridge CB10 1SD, UK <a href="http://www.ensemblgenomes.org/" target="_blank">http://www.ensemblgenomes.org/</a><br>
<br>
<br>
<br>
<br>
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