Question: Local Ucsc Mirror: Segmentation Fault And Other Problems
gravatar for Devst
8.3 years ago by
Devst20 wrote:

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?

genome local ucsc • 2.4k views
ADD COMMENTlink written 8.3 years ago by Devst20
gravatar for Pascal
8.3 years ago by
Pascal150 wrote:

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

ADD COMMENTlink modified 5 months ago by RamRS25k • written 8.3 years ago by Pascal150

nice link, hadn't seen this before

ADD REPLYlink written 8.3 years ago by Casey Bergman18k

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.

ADD REPLYlink written 8.2 years ago by Devst20

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.

ADD REPLYlink written 8.2 years ago by Pascal150
gravatar for Eric Fournier
8.3 years ago by
Eric Fournier1.4k
Quebec, Canada
Eric Fournier1.4k wrote:

Problems mirroring the UCSC Genome browser should be sent to the genome mirror mailing list,

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.

ADD COMMENTlink written 8.3 years ago by Eric Fournier1.4k

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.

ADD REPLYlink written 8.2 years ago by Devst20
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