AMR finder

[namdeka]

https://github.com/ncbi/amr/blob/master/README.md

[tonykew]

Test build completed - more info to follow...

[tonykew]

AMR finder plus have been published to the CCR software stack.

vortex1$ module spider amrfinder
----------------------------------------------------------------------------
  amrfinderplus: amrfinderplus/3.11.18
----------------------------------------------------------------------------
    Description:
      This software and the accompanying database are designed to find
      acquired antimicrobial resistance genes and some point mutations in
      protein or assembled nucleotide sequences.

    You will need to load all module(s) on any one of the lines below before the "amrfinderplus/3.11.18" module is available to load.

      gcc/11.2.0  openmpi/4.1.1
[...] 
vortex1$ module load gcc/11.2.0 openmpi/4.1.1 amrfinderplus/3.11.18
vortex1$ 

Binaries available in the PATH after loading the module:

vortex1$ ls ${EBROOTAMRFINDERPLUS}
amrfinder         amr_report    easybuild    fasta_check    gff_check
amrfinder_update  dna_mutation  fasta2parts  fasta_extract
vortex1$ 

e.g.

vortex1$ amrfinder --help
Identify AMR and virulence genes in proteins and/or contigs and print a report

DOCUMENTATION
    See https://github.com/ncbi/amr/wiki for full documentation

UPDATES
    Subscribe to the amrfinder-announce mailing list for database and software update notifications:
    https://www.ncbi.nlm.nih.gov/mailman/listinfo/amrfinder-announce

USAGE:   amrfinder [--update] [--force_update] [--protein PROT_FASTA] [--nucleotide NUC_FASTA] [--gff GFF_FILE] [--annotation_format ANNOTATION_FORMAT] [--database DATABASE_DIR] [--database_version] [--ident_min MIN_IDENT] [--coverage_min MIN_COV] [--organism ORGANISM] [--list_organisms] [--translation_table TRANSLATION_TABLE] [--plus] [--report_common] [--report_all_equal] [--name NAME] [--print_node] [--mutation_all MUT_ALL_FILE] [--output OUTPUT_FILE] [--protein_output PROT_FASTA_OUT] [--nucleotide_output NUC_FASTA_OUT] [--nucleotide_flank5_output NUC_FLANK5_FASTA_OUT] [--nucleotide_flank5_size NUC_FLANK5_SIZE] [--blast_bin BLAST_DIR] [--hmmer_bin HMMER_DIR] [--quiet] [--pgap] [--gpipe_org] [--parm PARM] [--threads THREADS] [--debug] [--log LOG]
HELP:    amrfinder --help or amrfinder -h
VERSION: amrfinder --version
[...]
vortex1$