jhangyu

Auto download list from NCBI

May 25th, 2018
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  1. destination=/mnt/biogalaxy/2017_Tilapia_genome/illumina/hiseq2000/
  2. local=/data/fastq/tilapia/NCBI/illumina/hiseq2000
  3. while read id
  4. do
  5.     fastq-dump --gzip ${id}
  6.     pids="$pids $!"
  7.     echo
  8.     wait $pids
  9. done < idlist.txt
  10.  
  11. cd /mnt/biogalaxy
  12. cd {$local}
  13.  
  14. while read id
  15. do
  16.     cp ${id}.fastq.gz {$destination}
  17.     pids="$pids $!"
  18.     echo
  19.     wait $pids
  20. done < idlist.txt
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