Painful Experience on Building Local UCSC Genome Browser

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I want to install a UCSC genome browser on my ubuntu workstation, to integrate and display the genomes , mostly plant genomes, with related annotations and NGS data, e.g. RNA-seq, methylation, SNPs, synteny, genome alignment, and etc.. There are also other genome browsers, but UCSC is my favorite and can meet my needs.

I spent a couple of workdays building from sources and adding custom genomes. The browser is based on mysql and apache which I don’t know much about, so It’s not surprising I encountered tons of problems. Thank google and other kind people who posted their experiences. I feel sorry that I cannot do the same thing as them, but at least I would like to share some resources and tips.

1) Read the README files in the sources, and follow the instructions. (You’d better understand them.)

2) The wiki site is very helpfull.

3) Other people’s experiences. (1 and 2)

4) If top bar is not showing, add the following code in apach2 conf file. (/etc/apache2/apache2.conf on my machine) 5) Mysql loading local file issue in hgLOAD* scripts. I tried different solutions, but only one worked for me. I logged into mysql and run the loading command if the error appears.

6) Stop mysql before rsync mysql files from UCSC server.

7) Most mysql problems were caused by permission settings.