Mercurial > repos > dcouvin > resfinder4
comparison resfinder/scripts/install_resfinder.sh @ 0:55051a9bc58d draft default tip
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| author | dcouvin |
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| date | Mon, 10 Jan 2022 20:06:07 +0000 |
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| -1:000000000000 | 0:55051a9bc58d |
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| 1 ### Install ResFinder 4.0 ### | |
| 2 | |
| 3 # Dependencies: | |
| 4 # NCBIs BLAST (module load ncbi-blast/2.6.0+) | |
| 5 pip3 install biopython | |
| 6 pip3 install tabulate | |
| 7 pip3 install cgecore | |
| 8 | |
| 9 # Install | |
| 10 git clone -b 4.0 https://bitbucket.org/genomicepidemiology/resfinder.git | |
| 11 git clone -b new_naming https://bitbucket.org/genomicepidemiology/pointfinder_db.git resfinder/db_pointfinder | |
| 12 git clone https://bitbucket.org/genomicepidemiology/resfinder_db.git resfinder/db_resfinder | |
| 13 git clone https://bitbucket.org/genomicepidemiology/kma.git resfinder/cge/kma | |
| 14 cd resfinder/cge/kma && make | |
| 15 cd ../.. | |
| 16 mkdir db_resfinder/kma_indexing | |
| 17 cge/kma/kma_index -i db_resfinder/fusidicacid.fsa -o db_resfinder/kma_indexing/fusidicacid | |
| 18 cge/kma/kma_index -i db_resfinder/phenicol.fsa -o db_resfinder/kma_indexing/phenicol | |
| 19 cge/kma/kma_index -i db_resfinder/glycopeptide.fsa -o db_resfinder/kma_indexing/glycopeptide | |
| 20 cge/kma/kma_index -i db_resfinder/trimethoprim.fsa -o db_resfinder/kma_indexing/trimethoprim | |
| 21 cge/kma/kma_index -i db_resfinder/oxazolidinone.fsa -o db_resfinder/kma_indexing/oxazolidinone | |
| 22 cge/kma/kma_index -i db_resfinder/tetracycline.fsa -o db_resfinder/kma_indexing/tetracycline | |
| 23 cge/kma/kma_index -i db_resfinder/quinolone.fsa -o db_resfinder/kma_indexing/quinolone | |
| 24 cge/kma/kma_index -i db_resfinder/nitroimidazole.fsa -o db_resfinder/kma_indexing/nitroimidazole | |
| 25 cge/kma/kma_index -i db_resfinder/fosfomycin.fsa -o db_resfinder/kma_indexing/fosfomycin | |
| 26 cge/kma/kma_index -i db_resfinder/aminoglycoside.fsa -o db_resfinder/kma_indexing/aminoglycoside | |
| 27 cge/kma/kma_index -i db_resfinder/macrolide.fsa -o db_resfinder/kma_indexing/macrolide | |
| 28 cge/kma/kma_index -i db_resfinder/sulphonamide.fsa -o db_resfinder/kma_indexing/sulphonamide | |
| 29 cge/kma/kma_index -i db_resfinder/rifampicin.fsa -o db_resfinder/kma_indexing/rifampicin | |
| 30 cge/kma/kma_index -i db_resfinder/colistin.fsa -o db_resfinder/kma_indexing/colistin | |
| 31 cge/kma/kma_index -i db_resfinder/beta-lactam.fsa -o db_resfinder/kma_indexing/beta-lactam | |
| 32 cge/kma/kma_index -i db_pointfinder/campylobacter/*.fsa -o db_pointfinder/campylobacter/campylobacter | |
| 33 cge/kma/kma_index -i db_pointfinder/escherichia_coli/*.fsa -o db_pointfinder/escherichia_coli/escherichia_coli | |
| 34 cge/kma/kma_index -i db_pointfinder/enterococcus_faecalis/*.fsa -o db_pointfinder/enterococcus_faecalis/enterococcus_faecalis | |
| 35 cge/kma/kma_index -i db_pointfinder/enterococcus_faecium/*.fsa -o db_pointfinder/enterococcus_faecium/enterococcus_faecium | |
| 36 cge/kma/kma_index -i db_pointfinder/neisseria_gonorrhoeae/*.fsa -o db_pointfinder/neisseria_gonorrhoeae/neisseria_gonorrhoeae | |
| 37 cge/kma/kma_index -i db_pointfinder/salmonella/*.fsa -o db_pointfinder/salmonella/salmonella | |
| 38 cge/kma/kma_index -i db_pointfinder/mycobacterium_tuberculosis/*.fsa -o db_pointfinder/mycobacterium_tuberculosis/mycobacterium_tuberculosis | |
| 39 | |
| 40 python3 test/functional_test.py | |
| 41 |