Bacting := acting as the Bioclipse TNG
How to cite
If you use this software, please cite the Bioclipse 2 paper.
First, you need a working Maven installation and then install this software:
mvn clean install
Bumping the version
Use this command to change the version number (and update BioclipseManager.version()):
mvn versions:set -DgroupId=io.github.egonw.bacting -DartifactId=bioclipse-* -DoldVersion=2.8.0 -DnewVersion=126.96.36.199 mvn versions:set -DgroupId=io.github.egonw.bacting -DartifactId=managers-* -DoldVersion=0.0.4 -DnewVersion=0.0.5-SNAPSHOT
It can be used in Groovy by including the Bacting managers you need:
@Grab(group='io.github.egonw.bacting', module='managers-cdk', version='0.0.5') workspaceRoot = "." def cdk = new net.bioclipse.managers.CDKManager(workspaceRoot); println cdk.fromSMILES("COC")
For the time being, the API is incomplete. Particularly, manager functionality around graphical UX in the original Bioclipse may never be implemented. Each Bacting release will implement more APIs and the release notes will mention which managers and which methods have been added.
For a description of the API, I refer to the book A lot of Bioclipse Scripting Language examples that Jonathan and I compiled.
All Bacting scripts will be backwards compatible with Bioclipse. If you want to install Bioclipse and see its wonderful UX in actions, download Bioclipse 2.6.2 here.
Using SNAPSHOT versions
You may need to occassionally delete the modules cached by Groovy, by doing something like, to remove earlier SNAPSHOT versions:
\rm -Rf ~/.groovy/grapes/net.bioclipse.managers/
Copyright and authors
All code in the
/bioclipse/ folder contains Bioclipse 2 code and the headers of the individual
source code files describe who contributed to that code of that class, but unfortunately this code
ownership is not always clear. I refer to the various Bioclipse code repositories
for the git history for more information.