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 |