--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/resfinder/scripts/install_resfinder.sh	Mon Jan 10 20:06:07 2022 +0000
@@ -0,0 +1,41 @@
+### Install ResFinder 4.0 ###
+
+# Dependencies:
+# NCBIs BLAST (module load ncbi-blast/2.6.0+)
+pip3 install biopython
+pip3 install tabulate
+pip3 install cgecore
+
+# Install
+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
+
+python3 test/functional_test.py
+