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Alternative accession data download script for Krona for when NCBI FTP breaks
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| #!/bin/bash | |
| # Alternative download script for Krona (https://github.com/marbl/Krona) for when (always) NCBI FTP breaks. | |
| # Built for krona 2.8.1 | |
| pushd [...]/opt/krona/taxonomy/accession2taxid | |
| FILES="dead_nucl.accession2taxid dead_prot.accession2taxid dead_wgs.accession2taxid nucl_gb.accession2taxid nucl_wgs.accession2taxid prot.accession2taxid" | |
| for f in $FILES; do | |
| wget -c https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/$f.gz | |
| wget -c https://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/$f.gz.md5 | |
| s1=$(cat $f.gz.md5 | cut -f1) | |
| s2=$(md5sum $f.gz | cut -f1) | |
| echo $f $s1 $s2 >> md5 | |
| done; | |
| [...]/opt/krona/updateAccessions.sh --only-build --preserve | |
| popd |
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