extracting ORF feature using txCdsPredict

[zgs17]

Hi, I use txCdsPredict to extract ORF feature, but I got the following error:
data/txCdsPredict: error while loading shared libraries: libmysqlclient.so.16: cannot open shared object file: No such file or directory
Would you please tell me how to solve this problem? Thank you.

[xypan1232]

I guess you need install MYSQL on your PC.

[mstricker13]

The issue is, that txCdsPredict has been compiled using the library libmysqlclient.so.16, which is now quite old. Simply installing mysql will install a newer version which is not compatible with this one.
There are two approaches to solve it:

1. Somehow manage to install this old version. I wasn't able to do that on my ubuntu system.
2. Compile it yourself and then replace the not working version with your version (this worked for me).

• In order to do that, you have to download the sources for the command line tools of the genome browser. You can find them here: http://hgdownload.cse.ucsc.edu/admin/exe/ (I downloaded the newest version called 'userApps.v390.src')
• unpack it and read the readme to know which requirements you have to install
• build it according to the readme
• This will unfortunetly not build txCdsPredict. In order to build that, you have to head to its location in a terminal with: cd userApps/kent/src/hg/txCds/txCdsPredict
• Then you have to build it with writting 'make' in your terminal
• Now you can find it at userApps/bin
• Replace the not working version at data/txCdsPredict with your newly compiled one.