本地KEGG功能注释工具
https://www.genome.jp/tools/kofamkoala/
1.下载数据库软件
wget -bc ftp://ftp.genome.jp/pub/db/kofam/ko_list.gz
wget -bc ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz
gunzip ko_list.gz
tar xvzf profiles.tar.gz
ftp://ftp.genome.jp/pub/tools/kofam_scan/kofam_scan-1.3.0.tar.gz
tar zxvf kofam_scan-1.3.0.tar.gz
2.下载安装依赖
安装 Ruby(http://www.ruby-lang.org/zh_cn/)
安装 HMMER(http://www.hmmer.org/)
安装 GNU Parallel(https://www.gnu.org/software/parallel/)
3.编辑软件配置
cp config-template.yml config.yml
An example of config.yml is as follows:
# Path to your KO-HMM database
# A database can be a .hmm file, a .hal file or a directory in which
# .hmm files are. Omit the extension if it is .hal or .hmm file
profile: /home/software/KEGG_annotation/kofam_scan-1.3.0/db/profiles/
# Path to the KO list file
ko_list: /home/software/KEGG_annotation/kofam_scan-1.3.0/db/ko_list
# Path to an executable file of hmmsearch
# You do not have to set this if it is in your $PATH
hmmsearch: /usr/local/bin/hmmsearch
# Path to an executable file of GNU parallel
# You do not have to set this if it is in your $PATH
parallel: /usr/local/bin/parallel
# Number of hmmsearch processes to be run parallelly
cpu: 20