Case I: download ucsc stand alone applications:

There are many cool features at UCSC, and I started to learn them and hopefully remember them also.

UCSC stand-alone applications

It seems like a very simple question, but I can’t download the executable with “wget”, but rather get “index.html”. Looked at a few good sites superuser, but none of them seem to be helpful.

It turns out, the robot.txt disallowed some url. Tried to overwrite this file and the download was just fine. Thanks to Xu, Hong, my colleague who helped me with this. To do this, we need three steps

[xuh2@superhong ucsc]$ wget -r -np http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/
[xuh2@superhong ucsc]$ echo > hgdownload.cse.ucsc.edu/robots.txt
[xuh2@superhong ucsc]$ wget -r -np http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ -nc

Here is another good wget help site. Basically, using something like “wget -e robots=off –wait 0.25 http://your.site.here”

One last step, I had to chmod 755 to restore them to executable.

Case II: download ucsc annotation:

There are plenty of information at ucsc sites , here I am learning how to download psl format db

here is a good link

another good link

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