CPC - Coding Potential Calculator

quick links

This guide is about how to install CPC package on your local machine.
And firstly, you might want to go to the Download Page.

Pre-requisite
- NCBI BLAST package: a local version could be downloaded from http://www.ncbi.nlm.nih.gov/blast/
- A relatively comprehensive protein database. UniRef90 and NCBI nr should be both okay. The database should be named as "prot_db", and put under the data/ sub-directory.
Getting CPC source-code.

Now surppose your username is tom and your hostname is jerry, and so the prompt might be tom@jerry$ . Using the following command to get CPC standalone package.
tom@jerry$ wget http://cpc.cbi.pku.edu.cn/download/cpc-0.9.tar.gz
Then use this command to unpackage the compressed source-code package.
tom@jerry$ gzip -dc cpc-0.9.tar.gz | tar xf -
or just
tom@jerry$ tar -zxf cpc-0.9.tar.gz
Then complie and install the CPC package.
tom@jerry$ cd cpc-0.9 tom@jerry$ export CPC_HOME="$PWD" tom@jerry$ cd libs/libsvm tom@jerry$ gzip -dc libsvm-2.8.1.tar.gz | tar xf - tom@jerry$ cd libsvm-2.8.1 tom@jerry$ make clean && make tom@jerry$ cd ../.. tom@jerry$ gzip -dc estate.tar.gz | tar xf - tom@jerry$ cd estate tom@jerry$ make clean && make
Format BLAST database named as "prot_db", and put under the $CPC_HOME/data/ directory.
Run CPC
tom@jerry$ cd $CPC_HOME tom@jerry$ bin/run_predict.sh (input_seq) (result_in_table) (working_dir) (result_evidence)