Instructions on using the antiSMASH standalone-lite docker container. This is a smaller container with some extra work required to download and prepare the databases. For a more convenient container where all of this is included already, check out the install guide for the full standalone container.
Setup & Install
As this is a guide for running antiSMASH in Docker, make sure to install Docker first. Because Docker needs a Linux kernel to run, this works fastest on a Linux host with a recent kernel, because then you can avoid the overhead of a virtual machine. antiSMASH needs at least 8 GB of RAM, so make sure to provide that amount if you go with a virtual machine.
To "install" antiSMASH, grab the wrapper shell script off our Bitbucket repository and put it into your path as an executable, like so:
mkdir ~/bin # only needed if you don't have a bin directory in your $HOME
curl https://bitbucket.org/antismash/docker/raw/HEAD/standalone-lite/run_antismash > ~/bin/run_antismash
chmod a+x ~/bin/run_antismash
If you had to create your ~/bin directory, you might want to log off and on again to get ~/bin added to your path.
Now, you need to prepare the databases for PFAM and ClusterBlast. On my machine,
they live in /data/databases/pfam and /data/databases/clusterblast,
respectively. The container expects a single volume that contains the pfam and
clusterblast subdirectories. If you want to change the default location of
/data/databases, you need to modify the DATABASE_DIR variable in the
run_antismash script. For the rest of this guide I'm going to assume you went
with the default.
Installing the PFAM database
You need the hmmer 3.1 hmmpress tool in your path for this to work.
mkdir -p /data/databases/pfam && cd /data/databases/pfam
curl ftp://ftp.sanger.ac.uk/pub/databases/Pfam/current_release/Pfam-A.hmm.gz > Pfam-A.hmm.gz
gunzip Pfam-A.hmm.gz
hmmpress Pfam-A.hmm
Installing the ClusterBlast database
You need GNU tar with xz compression support in your path for this to work.
mkdir -p /data/databases/clusterblast && cd /data/databases/clusterblast
curl https://bitbucket.org/antismash/antismash/downloads/clusterblast_dmnd07.tar.xz > clusterblast_dmnd07.tar.xz
tar -xJf clusterblast_dmnd07.tar.xz
Check the installation
To check if everything works as expected, try running run_antismash . .
--version, you should see the antiSMASH version being printed, e.g. antiSMASH
3.0.3. On the first run of the script, this might take a while as docker will
need to download the container, and that's a couple of GB in size.
If you get an error like run_antismash: command not found, you need to
make sure the run_antismash script is in your path and executable. I'll
explain why you need to add the . . before the --version next.
Running antiSMASH
The run_antismash wrapper script takes a number of parameters that will be
passed to antiSMASH after some further processing. Basically, you need to pass
the input file and the output directory, so both can be added to the container.
This is required, or the antiSMASH program running inside of the container
wouldn't be able to see the input file or write the output file anywhere you can
retrieve it. Additionally, any further parameters will be passed to antiSMASH
unchanged. So to recap, running antiSMASH works like this:
run_antismash /my/input/file.gbk /my/antismash/results --parameters --for --antismash
Example: Get the antiSMASH version
The actual antiSMASH script doesn't need any input or output files to just print the version, but the wrapper script will get sad if you don't provide those. So, the way to get the antiSMASH version is:
run_antismash . . --version
Example: List available command line options
Using the same trick as previously, we can get antisMASH to print available command line options.
run_antismash . . --help
Example: Run antiSMASH on Streptomyces coelicolor with KnownClusterBlast
And finally let's run some real antiSMASH job. My input file is on the /data
drive, I want the result to go to my ~/as_results directory. As parameters,
I'll just go with --knownclusterblast for now.
run_antismash /data/genomes/current/Bacteria/Streptomyces_coelicolor_A3_2/NC_003888.gbk ~/as_results --knownclusterblast
The output will be in ~/as_results/NC_003888.
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