Working document for Scala/GATK/Queue setup guide.

gistfile1.txt

*----------------------------------
* Setting up git
*----------------------------------

Clone gatk git repo

Add the main gatk repo as a upstream remote repo:
git remote add upstream https://github.com/broadgsa/gatk.git

Change the remote of the master branch to upstream. .git/config should look like this.

.git/config
[core]
        repositoryformatversion = 0
        filemode = true
        bare = false
        logallrefupdates = true
[remote "origin"]
        fetch = +refs/heads/*:refs/remotes/origin/*
        url = [email protected]:johandahlberg/gatk.git
[branch "master"]
        remote = upstream
        merge = refs/heads/master
[remote "upstream"]
        url = https://github.com/broadgsa/gatk.git
        fetch = +refs/heads/*:refs/remotes/upstream/*

Checkout the origin/devel branch

git checkout origin/devel -b devel

*----------------------------------
* Setting up Eclipse
*----------------------------------

Install eclipse

Use a scala IDE release which is compatible with the scala version in GATK:
http://download.scala-ide.org/releases-28/stable/site

Install EGit for eclipse
Just search for git in "Install New Software"

Install IvyIDE:
http://www.apache.org/dist/ant/ivyde/updatesite

Import the gatk project from your local repo, using import from git and then using the scala new project wizard to create a new project.
    Change default output folder to gatk/build

Add ivy.xml as a Ivy library

-------------------------------------------------------------------------
New notes:
Have not been able to confirm this yet, but it seems like going to the properties of the ivy container and enableing project specific settings does solve some of the issues described below.
-------------------------------------------------------------------------


IvyDE will not be able to resolve some dependencies. To be specific, the error message will look like the following:

Some projects fail to be resolved
Impossible to resolve dependencies of org.broadinstitute#Sting;working@mm-xdahljo01
unresolved dependency: net.sf#picard;latest.integration: not found
unresolved dependency: org.broad#tribble;latest.integration: not found
unresolved dependency: net.sf#sam;latest.integration: not found
unresolved dependency: net.sf.gridscheduler#drmaa;latest.integration: not found
unresolved dependency: edu.mit.broad#picard-private-parts;latest.integration: not found

These dependencies can be downloaded by building from the commandline once (this manages to download the dependencies). Do this by going to the gatk folder and type "ant". This will place the dependency in the lib folder. Go to "configure build path" in eclipse and and the missing jars to the classpath manually.

Eclipse will still be complaining that it cannot resolve the dependencies.

It might also complain about having more than one scala library in the build path. In that case remove the "Scaka library" from the build path. I might then say that i cannot fin a Scala library on the classpath, but don't worry. It will work any way.