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A scripting language for automatically creating BioMarts.

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MartScript

MartScript is a simple non-branching imperative scripting language for creating BioMarts (see www.biomart.org) automatically (i.e. non-interactively). The language supports

  • extending Ensembl databases with custom data
  • automation of MartBuilder/MartEditor functionality
  • the creation and execution of a BioMart's SQL-commands

This is a fully functional release of MartScript as a beta version, mainly due to the lack of documentation and some minor cosmetic issues. However, we used MartScript in production to create: www.pubmed2ensembl.org

Executing MartScripts

Clone this repo or download the ZIP file. With Java 1.6 and Perl 5.12 (or newer) run the following:

for jar in lib/*.jar ; do export CLASSPATH=$CLASSPATH:`pwd`/$jar ; done
cd bin
java -Xmx3G org.bergmanlab.martscript.MartScript yourscript.mscr

Re-compiling MartScript

MartScript's Java classes can be recompiled using:

for jar in lib/*.jar ; do export CLASSPATH=$CLASSPATH:`pwd`/$jar ; done
javac -source 1.4 -d bin -sourcepath src src/org/bergmanlab/martscript/MartScript.java

Supporting Software

MartScript depends on partially modified code of MartBuilder as well as as JAR files of several libraries that from the BioMart project, which are redistributed here. MartBuilder, MartEditor and the JAR-packaged files are released under LGPL.

License

MartScript is released under the LGPL (see LICENSE).

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