准备工作
1.安装好conda以及mamba
2.建立一个环境，命名为resfinder
conda create -n resfinder
激活环境
source activate resfinder
开始安装
1.准备安装脚本，复制以下代码至一个txt文件中，保存后修改文件名为"install_resfinder.sh"，代码修改自：
resfinder/install_resfinder.sh at master · cadms/resfinder (github.com)
赋予权限：
chmod 777 install_resfinder.sh
运行：
sh ./install_resfinder.sh
途中需要确认conda的软件安装，选择"Y"即可。
### Install ResFinder 4.0 ###
# 依赖软件安装:如果有装mamba的话则修改为mamba安装
conda install blast cgecore tabulate biopython python==3.8.13 -c bioconda
#resfinder安装及数据库的部署
git clone -b 4.0 https://bitbucket.org/genomicepidemiology/resfinder.git
git clone -b new_naming https://bitbucket.org/genomicepidemiology/pointfinder_db.git resfinder/db_pointfinder
git clone https://bitbucket.org/genomicepidemiology/resfinder_db.git resfinder/db_resfinder
git clone https://bitbucket.org/genomicepidemiology/kma.git resfinder/cge/kma
cd resfinder/cge/kma && make
cd ../..
mkdir db_resfinder/kma_indexing
cge/kma/kma_index -i db_resfinder/fusidicacid.fsa -o db_resfinder/kma_indexing/fusidicacid
cge/kma/kma_index -i db_resfinder/phenicol.fsa -o db_resfinder/kma_indexing/phenicol
cge/kma/kma_index -i db_resfinder/glycopeptide.fsa -o db_resfinder/kma_indexing/glycopeptide
cge/kma/kma_index -i db_resfinder/trimethoprim.fsa -o db_resfinder/kma_indexing/trimethoprim
cge/kma/kma_index -i db_resfinder/oxazolidinone.fsa -o db_resfinder/kma_indexing/oxazolidinone
cge/kma/kma_index -i db_resfinder/tetracycline.fsa -o db_resfinder/kma_indexing/tetracycline
cge/kma/kma_index -i db_resfinder/quinolone.fsa -o db_resfinder/kma_indexing/quinolone
cge/kma/kma_index -i db_resfinder/nitroimidazole.fsa -o db_resfinder/kma_indexing/nitroimidazole
cge/kma/kma_index -i db_resfinder/fosfomycin.fsa -o db_resfinder/kma_indexing/fosfomycin
cge/kma/kma_index -i db_resfinder/aminoglycoside.fsa -o db_resfinder/kma_indexing/aminoglycoside
cge/kma/kma_index -i db_resfinder/macrolide.fsa -o db_resfinder/kma_indexing/macrolide
cge/kma/kma_index -i db_resfinder/sulphonamide.fsa -o db_resfinder/kma_indexing/sulphonamide
cge/kma/kma_index -i db_resfinder/rifampicin.fsa -o db_resfinder/kma_indexing/rifampicin
cge/kma/kma_index -i db_resfinder/colistin.fsa -o db_resfinder/kma_indexing/colistin
cge/kma/kma_index -i db_resfinder/beta-lactam.fsa -o db_resfinder/kma_indexing/beta-lactam
cge/kma/kma_index -i db_pointfinder/campylobacter/*.fsa -o db_pointfinder/campylobacter/campylobacter
cge/kma/kma_index -i db_pointfinder/escherichia_coli/*.fsa -o db_pointfinder/escherichia_coli/escherichia_coli
cge/kma/kma_index -i db_pointfinder/enterococcus_faecalis/*.fsa -o db_pointfinder/enterococcus_faecalis/enterococcus_faecalis
cge/kma/kma_index -i db_pointfinder/enterococcus_faecium/*.fsa -o db_pointfinder/enterococcus_faecium/enterococcus_faecium
cge/kma/kma_index -i db_pointfinder/neisseria_gonorrhoeae/*.fsa -o db_pointfinder/neisseria_gonorrhoeae/neisseria_gonorrhoeae
cge/kma/kma_index -i db_pointfinder/salmonella/*.fsa -o db_pointfinder/salmonella/salmonella
cge/kma/kma_index -i db_pointfinder/mycobacterium_tuberculosis/*.fsa -o db_pointfinder/mycobacterium_tuberculosis/mycobacterium_tuberculosis
问题
正常来说按照以上的来是没有问题了。一开始我遇到的问题是安装完成后运行resfinder提示
"AttributeError: module 'collections' has no attribute 'MutableSet'"
查询后发现应该是python版本的问题，所以降级python从3.10至3.8.13（上面已经指定安装的python版本），之后就可以正常使用resfinder了。
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