Mercurial > repos > iuc > bracken

annotate test-data/reproduce_test_data.sh @ 2:a5145865e467 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 2a7a1f987c8fd07ae19140dd0ae86ff2a710de52"
author iuc
date Thu, 17 Oct 2019 15:50:37 -0400
parents b7b1c8bf7ae0
children
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b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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1 #!/bin/bash
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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3 # This script produces a small kraken2 database containing only a ~1kb portion each of a salmonella and ecoli genome
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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4 # It requires kraken2, art and entrez-direct (all available on bioconda)
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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5 kraken2-build --db test_db --download_taxonomy
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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6 mv test_db/taxonomy/nucl_gb.accession2taxid test_db/taxonomy/nucl_gb.accession2taxid_full
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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7 grep -e 'NC_003198.1' -e 'NC_011750.1' test_db/taxonomy/nucl_gb.accession2taxid_full > test_db/taxonomy/nucl_gb.accession2taxid
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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8 esearch -db nucleotide -query "NC_003198.1" | efetch -format fasta > NC_003198.1.fasta
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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9 esearch -db nucleotide -query "NC_011750.1" | efetch -format fasta > NC_011750.1.fasta
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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10 head -n 14 NC_003198.1.fasta > NC_003198.1_1kb.fasta
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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11 head -n 14 NC_011750.1.fasta > NC_011750.1_1kb.fasta
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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12 kraken2-build --db test_db --add-to-library NC_003198.1_1kb.fasta
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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13 kraken2-build --db test_db --add-to-library NC_011750.1_1kb.fasta
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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14 kraken2-build --db test_db --build
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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16 # Simulate 100bp reads from ~1kb portions of genomes
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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17 art_illumina -sam -i NC_011750.1_1kb.fasta -p -m 300 -f 10 -s 10 -l 100 -o NC_011750.1_simulated_R
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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18 art_illumina -sam -i NC_003198.1_1kb.fasta -p -m 300 -f 10 -s 10 -l 100 -o NC_003198.1_simulated_R
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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20 # Generate kraken reports
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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21 kraken2 --db test_db --report NC_011750.1_simulated_kraken_report.txt --paired NC_011750.1_simulated_R1.fastq NC_011750.1_simulated_R2.fastq
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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22 kraken2 --db test_db --report NC_003198.1_simulated_kraken_report.txt --paired NC_003198.1_simulated_R1.fastq NC_003198.1_simulated_R2.fastq
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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24 # Build bracken kmer distribution files using default kmer-len=35 and read-len=100
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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25 bracken-build -d test_db
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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27 #
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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28 # est_abundance.py --kmer_distr test_db/database100mers.kmer_distrib --level S -i NC_003198.1_simulated_kraken_report.txt -o NC_003198.1_simulated_bracken_report.txt
b7b1c8bf7ae0 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bracken commit 851f81495c875ac09d936537ffd2b32e6af2c8c5"
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29 # est_abundance.py --kmer_distr test_db/database100mers.kmer_distrib --level S -i NC_011750.1_simulated_kraken_report.txt -o NC_011750.1_simulated_bracken_report.txt