介绍

下载

  1. git clone https://github.com/eggnogdb/eggnog-mapper
  2. cd eggnog-mapper
  1. ./download_eggnog_data.py -h
  2. ## usage: download_eggnog_data.py [-h] [-D] [-F] [-P] [-M] [-H] [-d HMMER_DBS] [--dbname DBNAME] [-y] [-f] [-s] [-q]
  3. ##                                [--data_dir]
  4. ## 
  5. ## options:
  6. ##   -h, --help       show this help message and exit
  7. ##   -D               Do not install the diamond database (default: False)
  8. ##   -F               Install the novel families diamond and annotation databases, required for "emapper.py -m novel_fams"
  9. ##                    (default: False)
  10. ##   -P               Install the Pfam database, required for de novo annotation or realignment (default: False)
  11. ##   -M               Install the MMseqs2 database, required for "emapper.py -m mmseqs" (default: False)
  12. ##   -H               Install the HMMER database specified with "-d TAXID". Required for "emapper.py -m hmmer -d TAXID"
  13. ##                    (default: False)
  14. ##   -d HMMER_DBS     Tax ID of eggNOG HMM database to download. e.g. "-H -d 2" for Bacteria. Required if "-H". Available tax
  15. ##                    IDs can be found at http://eggnog5.embl.de/#/app/downloads. (default: None)
  16. ##   --dbname DBNAME  Tax ID of eggNOG HMM database to download. e.g. "-H -d 2 --dbname 'Bacteria'" to download Bacteria
  17. ##                    (taxid 2) to a directory named Bacteria (default: None)
  18. ##   -y               assume "yes" to all questions (default: False)
  19. ##   -f               forces download even if the files exist (default: False)
  20. ##   -s               simulate and print commands. Nothing is downloaded (default: False)
  21. ##   -q               quiet_mode (default: False)
  22. ##   --data_dir       Directory to use for DATA_PATH. (default: None)

使用

运行

参考