Update 2015-07-21 10:28 UTC: It seems a bit less magic is needed in the wrapper script.
After a longer discussion about the pros and cons of Docker at this year's BOSC, and a bit of complaining about the complexities of actually running docker in a recent blog post, I have decided to try this out for antiSMASH.
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/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.
To check if everything works as expected, try running
run_antismash . .
--version, you should see the antiSMASH version being printed, e.g.
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
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
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
All in all, I think this is a pretty nice way to get your feet wet with antiSMASH, but I have a couple of things that I find a bit annoying about this solution:
Some funky dance in the in-container wrapper script is required to make the output be owned by the user calling the script.Update: see below
- At the moment, the wrapper script doesn't allow to pass multiple input files.
- You always need to pass input and output directories to the wrapper script.
Update 2015-07-21 10:28
As Paolo Di Tommaso points out, it is
possible to specify the user the command within the container runs at with
@kaiblin No, I think you should be able to specify any uid/gid— Paolo Di Tommaso (@PaoloDiTommaso) July 21, 2015
The Docker documentation on docker run seems to imply otherwise:
The default user within a container is root (id = 0), but if the developer created additional users, those are accessible too.
But you can just use
-u $(id -u):$(id -g) in the
docker run command to
specify the current user's UID and GID, That works, and makes the wrapper
script less magic.
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