Hello, I have assemblies build on server, Cyverse to visualize newly sequenced genome of chromosome 1. However to visualize the genome in UCSC genome browser, I need to configure BLAT server, (a dedicated gf server) in Cyverse. To accomplish this, they have mentioned some guidelines i.e
Run two instances of gfServer from http://yourServer.yourInstitution.edu at the location of yourAssembly.2bit file, specifying a port that the gfServer will be accessible from for amino acid (-trans option) and DNA searches. Please note the -mask option will ignore all lower-case assembly sequence, which is the convention the UCSC Browser uses for masked sequence, so you may not want to include it from the example below.
When picking a port number, stick with numbers between 1024 and 49151. Anything less than 1024 is considered a system port and you'll need to be root in order to open it. Anything above 49151 is considered dynamic and randomly assigned.
For example, these two lines will specify port 17777 for DNA searches
and 17779 for amino acid searches and are run from the publicly accessibly directory location of yourAssembly.2bit file:
cd /genomes/yourAssembly gfServer start blatMachine 17777 -stepSize=5 -log=yourAssembly.untrans.log yourAssembly.2bit & gfServer start blatMachine 17779 -trans -mask -log=yourAssembly.untrans.log yourAssembly.2bit &
What does it mean? can anyone elaborate? About what kind of port they have mentioned here? where could i find it? how should i proceed?
This is fairly advanced web configuration what would be hard to teach/debug via a forum like this. Please ask CyVerse support to see if they can help you.