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1 ### Install ResFinder 4.0 ###
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2
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3 # Dependencies:
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4 # NCBIs BLAST (module load ncbi-blast/2.6.0+)
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5 pip3 install biopython
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6 pip3 install tabulate
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7 pip3 install cgecore
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8
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9 # Install
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10 git clone -b 4.0 https://bitbucket.org/genomicepidemiology/resfinder.git
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11 git clone -b new_naming https://bitbucket.org/genomicepidemiology/pointfinder_db.git resfinder/db_pointfinder
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12 git clone https://bitbucket.org/genomicepidemiology/resfinder_db.git resfinder/db_resfinder
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13 git clone https://bitbucket.org/genomicepidemiology/kma.git resfinder/cge/kma
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14 cd resfinder/cge/kma && make
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15 cd ../..
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16 mkdir db_resfinder/kma_indexing
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17 cge/kma/kma_index -i db_resfinder/fusidicacid.fsa -o db_resfinder/kma_indexing/fusidicacid
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18 cge/kma/kma_index -i db_resfinder/phenicol.fsa -o db_resfinder/kma_indexing/phenicol
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19 cge/kma/kma_index -i db_resfinder/glycopeptide.fsa -o db_resfinder/kma_indexing/glycopeptide
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20 cge/kma/kma_index -i db_resfinder/trimethoprim.fsa -o db_resfinder/kma_indexing/trimethoprim
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21 cge/kma/kma_index -i db_resfinder/oxazolidinone.fsa -o db_resfinder/kma_indexing/oxazolidinone
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22 cge/kma/kma_index -i db_resfinder/tetracycline.fsa -o db_resfinder/kma_indexing/tetracycline
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23 cge/kma/kma_index -i db_resfinder/quinolone.fsa -o db_resfinder/kma_indexing/quinolone
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24 cge/kma/kma_index -i db_resfinder/nitroimidazole.fsa -o db_resfinder/kma_indexing/nitroimidazole
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25 cge/kma/kma_index -i db_resfinder/fosfomycin.fsa -o db_resfinder/kma_indexing/fosfomycin
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26 cge/kma/kma_index -i db_resfinder/aminoglycoside.fsa -o db_resfinder/kma_indexing/aminoglycoside
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27 cge/kma/kma_index -i db_resfinder/macrolide.fsa -o db_resfinder/kma_indexing/macrolide
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28 cge/kma/kma_index -i db_resfinder/sulphonamide.fsa -o db_resfinder/kma_indexing/sulphonamide
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29 cge/kma/kma_index -i db_resfinder/rifampicin.fsa -o db_resfinder/kma_indexing/rifampicin
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30 cge/kma/kma_index -i db_resfinder/colistin.fsa -o db_resfinder/kma_indexing/colistin
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31 cge/kma/kma_index -i db_resfinder/beta-lactam.fsa -o db_resfinder/kma_indexing/beta-lactam
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32 cge/kma/kma_index -i db_pointfinder/campylobacter/*.fsa -o db_pointfinder/campylobacter/campylobacter
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33 cge/kma/kma_index -i db_pointfinder/escherichia_coli/*.fsa -o db_pointfinder/escherichia_coli/escherichia_coli
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34 cge/kma/kma_index -i db_pointfinder/enterococcus_faecalis/*.fsa -o db_pointfinder/enterococcus_faecalis/enterococcus_faecalis
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35 cge/kma/kma_index -i db_pointfinder/enterococcus_faecium/*.fsa -o db_pointfinder/enterococcus_faecium/enterococcus_faecium
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36 cge/kma/kma_index -i db_pointfinder/neisseria_gonorrhoeae/*.fsa -o db_pointfinder/neisseria_gonorrhoeae/neisseria_gonorrhoeae
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37 cge/kma/kma_index -i db_pointfinder/salmonella/*.fsa -o db_pointfinder/salmonella/salmonella
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38 cge/kma/kma_index -i db_pointfinder/mycobacterium_tuberculosis/*.fsa -o db_pointfinder/mycobacterium_tuberculosis/mycobacterium_tuberculosis
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39
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40 python3 test/functional_test.py
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41
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