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agough

NCBI ftp access - directory list

Sep 6th, 2016
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  1. #!/bin/bash
  2. hostname="ftp.ncbi.nlm.nih.gov"
  3. username="anonymous"
  4. password="a1.gough@qut.edu.au"
  5. ftp -vn $hostname << EOF
  6. quote USER $username
  7. quote PASS $password
  8. cd /genomes/refseq/bacteria/
  9. ls -1R ftpList.txt
  10. EOF
  11.  
  12. rsync --dry-run -avP --include "*.gbk" --include "*.fna" --include "*_*/" --exclude "*" ftp.ncbi.nih.gov::genomes/refseq/bacteria/ > ftplisting.txt
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