ILRI Research Computing

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====== abricate ======

Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB.


===== Information =====

  * Version: 1.0.1
  * Added: September, 2020
  * Link: https://github.com/tseemann/abricate

===== Usage =====

See which versions of abricate are available:
<code>$ module avail abricate</code>

Load one version into your environment and run it:
<code>$ module load abricate/1.0.1
$ abricate</code>

===== Installation ======

Notes from the sysadmin during installation:

<code>$ cd /tmp
$ git clone https://github.com/tseemann/abricate.git -b v1.0.1
$ cd abricate
$ grep -rh -oE "use Bio::.*$" bin/* | sort -u | awk '{print $2}'
Bio::Seq;
Bio::SeqIO;
$ mkdir perl5lib
$ cpanm -l perl5lib LWP::Simple Bio::Seq Bio::SeqIO JSON Path::Tiny --force
$ module load any2fasta/0.4.2
$ module load blast/2.7.1+
$ export PERL5LIB=perl5lib/lib/perl5
$ ./bin/abricate --check
$ ./bin/abricate --setupdb
$ ./bin/abricate test/assembly.fa
$ sudo mkdir -p /export/apps/abricate/1.0.1
$ sudo cp -r * /export/apps/abricate/1.0.1
</code>

**Note 1:** abricate only says that it requires BioPerl, but the BioPerl distribution frowns upon requiring the entire distribution. Here I have attempted to guess which modules are needed by checking the actual Perl "use" statements.

**Note 2:** You can try without %%''--force''%% if you want, but many Perl modules "bail out" during installation because one out of a few hundred (or thousand) obscure or comprehensive tests fail.