INSTALL

= 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. 

Download sbt-launch.jar 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:

  > test
  [info] == test-finish ==
  [info] Passed: : Total 84, Failed 0, Errors 0, Passed 84, Skipped 0
  [success] Successful.
  [info] Total time: 2 s

To check current versions and dependencies, see 

  https://github.com/bioscala/bioscala/blob/master/project/build.properties
  https://github.com/bioscala/bioscala/blob/master/project/build/bioscala.scala 

To try BioScala from other code, build the class files and add them to the
class path. A jar file will be provided in the future.

= Dependencies =

You need to have:

* BioJAVA:   Add the biojava.jar file to the class path (automatic by sbt)

* scalatest: Add the scalatest.jar file to the class path (automatic by sbt)

Optional are:

* BioRuby:   Unpack the BioRuby source and point the Ruby load path to the
             lib folder therein, e.g.:

               export RUBYLIB=~/local/lib/bioruby/lib

* JRuby:     Install jruby and add the big jruby-complete.jar file to the 
             class path, like jruby-complete-1.5.0.RC1.jar (check the version
             of your JRuby with the -v switch: jruby -v)

* BioJava3:

  biojava3-core-3.0-SNAPSHOT.jar       
  biojava3-alignment-3.0-SNAPSHOT.jar  
  biojava3-genome-3.0-SNAPSHOT.jar (optional)
  biojava3-phylo-3.0-SNAPSHOT.jar

if sbt has trouble finding jars, add them to the CLASSPATH, andOr check
./project/build/bioscala.scala, where the automatic load path is set.

= Trouble shooting =

- Error: value biojava is not a member of package org

biojava.jar is not in the class path. Run 'sbt update'

- Error: value should is not a member of java.lang.String
[error] "SegmentizeGappedSequence" should "handle two"

scalatest-ver.jar is not in the class path. Run 'sbt update'

- value ruby is not a member of package bio

jruby-ver.jar is not in the class path. Add the jar to the class path.