KofamKOALA - KEGG Orthology Search

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