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Scala Shell Ruby
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The goal of the BioScala project is to create a scalable and functional bioinformatics library; which can be used from Scala, Java, JRuby, Jython and Clojure; building on existing libraries available on the JAVA Virtual Machine (JVM), including BioJAVA and BioRuby. This is the place for the BioScala project under the liberal BSD license. See also the Tutorial http://monomorphic.org/bioscala/bioscala-tutorial.html design docs http://monomorphic.org/bioscala/bioscala-design.html and API docs http://monomorphic.org/bioscala/api/ This edition of BioScala has: - Strongly typed DNA, RNA Sequence, gapped and IUPAC ambiguous Sequence - Sequences contain lists of Nucleotide, AminoAcid, IUPAC, Gapped, Codon - Flexible Sequence user defined attributes - Transcription of DNA to RNA - Translation of (ambiguous) RNA to AA (using BioJava3) - Formats: . Iterator based FASTA reader and writer . Iterator based PAML (PHY) file format reader . Phylip reader/writer (using BioJava) - Alignments and attributes (work in progress) - A translation example of calling into BioRuby - A tutorial in ./doc/tutorial.txt BioScala uses the simple build tool (sbt) and behaviour driven development/unit testing. See the INSTALL file for more information. Please fork from https://github.com/bioscala/bioscala Pjotr Prins Mailing list: http://lists.thebird.nl/listinfo.cgi/bioscala-thebird.nl = INSTALL BioScala = It is rather easy to install a working repository of BioScala. The JVM is needed and sbt (simple build tool). First download BioScala from github with: git clone http://github.com/bioscala/bioscala.git Install Java. On Debian, for example: apt-get install sun-java6-jdk Install sbt (Simple build tool) from http://code.google.com/p/simple-build-tool/wiki/Setup. Install sbt and run it on the command line, for example # go to base bioscala directory cd bioscala # launch sbt java -Xmx512M -jar sbt-launch.jar # inside sbt type > update > compile > test sbt will automatically download Scala and related jars. Then it will compile and run the supplied tests. When running sbt from the command line in the base dir