conda安装kofamscan

官网的安装依赖的方法还是有些麻烦，直接用conda安装！避免报错~

下载数据库

mkdir -p /project/shenmy/biosoftware/kofamscan/db
cd /project/shenmy/biosoftware/kofamscan/db
wget ftp://ftp.genome.jp/pub/db/kofam/ko_list.gz  
wget ftp://ftp.genome.jp/pub/db/kofam/profiles.tar.gz  
gunzip ko_list.gz 
tar xvzf profiles.tar.gz  

安装环境

conda create  -n kofamscan -c bioconda kofamscan

运行

./exec_annotation -h
Usage: exec_annotation [options] <query>
  <query>                    FASTA formatted query sequence file
  -o <file>                  File to output the result  [stdout]
  -p, --profile <path>       Profile HMM database
  -k, --ko-list <file>       KO information file
  --cpu <num>                Number of CPU to use  [1]
  -c, --config <file>        Config file
  --tmp-dir <dir>            Temporary directory  [./tmp]
  -E, --e-value <e_value>    Largest E-value required of the hits
  -T, --threshold-scale <scale>
                             The score thresholds will be multiplied by this value
  -f, --format <format>      Format of the output [detail]
      detail:          Detail for each hits (including hits below threshold)
      detail-tsv:      Tab separeted values for detail format
      mapper:          KEGG Mapper compatible format
      mapper-one-line: Similar to mapper, but all hit KOs are listed in one line
  --[no-]report-unannotated  Sequence name will be shown even if no KOs are assigned
                             Default is true when format=mapper or mapper-all,
                             false when format=detail
  --create-alignment         Create domain annotation files for each sequence
                             They will be located in the tmp directory
                             Incompatible with -r
  -r, --reannotate           Skip hmmsearch
                             Incompatible with --create-alignment
  --keep-tabular             Neither create tabular.txt nor delete K number files
                             By default, all K number files will be combined into
                             a tabular.txt and delete them
  --keep-output              Neither create output.txt nor delete K number files
                             By default, all K number files will be combined into
                             a output.txt and delete them
                             Must be with --create-alignment