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Saturday, June 22, 2019

Bacting: Bioclipse from the command line

Source. Wikiepdia. Public Domain.
Because more and more cheminformatics I do is with Bioclipse scripts (see doi:10.1186/1471-2105-10-397) and that Bioclipse is currently unmaintained and has become hard to install, I decided to take the plunge and rewrite some stuff so that I could run the scripts from the command line. I wrote up the first release back in April.

Today, I release Bacting 0.0.5 (doi:10.5281/zenodo.3252486) which is the first release you can download from one of the main Maven repositories. I'm still far from a Maven or Grapes expert, but at least you can use Bacting now like this without actually having to download and compile the source code locally first:

@GrabResolver(
  name='ossrh',
  root='https://oss.sonatype.org/content/groups/public'
)
@Grab(
  group='io.github.egonw.bacting',
  module='managers-cdk',
  version='0.0.5'
)

workspaceRoot = "."
cdk = new net.bioclipse.managers.CDKManager(workspaceRoot);

println cdk.fromSMILES("CCO")

If you have been using Bacting before, then please note the change in groupId. If you want to check out all functionality, have a look at the changelogs of the releases.

If you want to cite Bacting, please cite the Bioclipse 2 paper and for the version release, follow the instructions on Zenodo. Pending an article. The Journal of Open Source Software? Sounds like a good idea!

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