Local Ucsc Mirror: Segmentation Fault And Other Problems

Question

[Devst]

Hi all,

I'm trying to install a local (partial) mirror of the UCSC Genome Browser on a Debian 6 (32 bit), but I encountered several problems along the way.

I was able to solve some of them, but now I'm stuck with some errors generated (I guess) by some cgi-bin executables.

One of them is generated by hgTables that gives me a lovely "Segmentation fault" on the command line (and a "Internal Server Error" page on localhost with Apache2).

Other CGI raise other different type of error, e.g. hgBlat gives me a "getaddrinfo() error on hostName=blat13: Name or service not known" on the browser, and so on.

So, has anyone experienced any kind of problems mirroring the UCSC and successful installed the mirror?

Answer 1

[Pascal]

This is not an answer to this question, but a good step-by-step tutorial can be found here.

[Casey Bergman]

nice link, hadn't seen this before

[Devst]

Actually I came across those problems following it. Well, don't misunderstand me, that's a really good tutorial. I guess that the situation I have is related somehow on my linux system. Thanks however.

[Pascal]

Ok, I did not knew that. Some time ago this worked fine for me, but I used Ubuntu 10.10 on a 64-bit machine.

Answer 2

[Eric Fournier]

Problems mirroring the UCSC Genome browser should be sent to the genome mirror mailing list, [e-mail]

The hgBlat error means that blat13 is not a valid host name in your domain. You have to modify the hgcentral database's blatServers table so that it points to a valid blat server. This means either running your own blat server, or asking UCSC permission to use theirs. Details on how to accomplish this are on the bottom of the minimal browser installation wiki page.

[Devst]

I sent an (another) email to the mailing list. I was a bit reluctant because the last response I got from them told me that they don't solve technical issues. That was a bit weird and disappointing (but, wathever). Thanks for the tip about blat, I will try it.