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download_sra.sh
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| #!/bin/bash | |
| SRA=$1 | |
| mkdir dl_$SRA | |
| cd dl_$SRA | |
| echo downloading $SRA | |
| DL_CMD="bionode-ncbi download sra $SRA" | |
| echo $DL_CMD | |
| eval $DL_CMD | |
| find . | grep -P '.sra$'>sra_list | |
| cat sra_list | xargs -P 8 -n 1 bionode-sra fastq-dump | |
| find *.fastq > fastq_list.txt | |
| echo completed download of $SRA in dl_$SRA and dumped these files $(cat fastq_list.txt) | |
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