Antibiotic Resistance Identification By Assembly

For how to use ARIBA, please see the ARIBA wiki page.

ARIBA has the following dependencies, which need to be installed:

• Python3 version >= 3.4
• R version >= 2.14.0
• The R package ape version >= 3.1
• Bowtie2 version >= 2.1.0
• CD-HIT version >= 4.6
• Samtools and BCFtools version >= 1.2
• MUMmer version >= 3.23
• SPAdes version >= 3.5.0
• Python2 version >= 2.7 (SPAdes needs python2)

ARIBA has the following optional dependencies. If they are installed, they will be used. Otherwise scaffolding and gap filling will be skipped.

• SSPACE-basic scaffolder
• GapFiller

Once the dependencies are installed, install ARIBA using pip:

pip3 install ariba

Alternatively, you can download the latest release from this github repository, or clone the repository. Then run the tests:

python3 setup.py test

If the tests all pass, install:

python3 setup.py install

By default, ARIBA will look for the dependencies in your $PATH, using the names in the table below. This behaviour can be overridden and point ARIBA to a specific program using environment variables. The environment variable is checked first and is used if it is set. Otherwise ARIBA looks in your $PATH for the default name. This applies to the following dependencies.

For example, you could specify an exact version of a Samtools executable that you compiled and downloaded in your home directory (assuming BASH):

export ARIBA_SAMTOOLS=$HOME/samtools-1.2/samtools

### Temporary files

ARIBA can temporarily make a large number of files whilst running, which are put in a temporary directory made by ARIBA. The total size of these files is small, but there can be a many of them. This can be a problem when running large numbers (100s or 1000s) of jobs simultaneously on the same file system. By default, ARIBA creates a temporary directory for these files inside the output directory of each run.

Each temporary directory is unique to one run of ARIBA, and is automatically deleted at the end of the run (even if ARIBA was killed by the user or crashed). The parent directory of the temporary directory can be changed using the environment variable $ARIBA_TMPDIR. The temporary directory for each run will be made inside $ARIBA_TMPDIR. For example,

export $ARIBA_TMPDIR=/tmp

will result in the creation of a new directory inside /tmp, which will have a name of the form

/tmp/ariba.tmp.abcdef

where the suffix abcdef is a random string of characters, chosen such that /tmp/ariba.tmp.abcdef does not already exist.

The temporary directory can also be changed using the option --tmp_dir when running ariba run. Using this option takes precedence over the environment variable $ARIBA_TMPDIR. If neither are set, then ARIBA creates the temporary directory inside the output directory given to ariba run.

The exception to the above is if the option --noclean is used. This forces the temporary directory to be placed in the output directory, and temporary files are kept. It is intended for debugging.

Please read the ARIBA wiki page for usage instructions.

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