From 7ff13b779b9f184640d105cf833bc794e509db01 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Mon, 27 Jun 2016 13:54:39 +0200
Subject: [PATCH] Add docs on using SBT
---
docs/developer/example-depends.md | 54 +++++++++++++++++++++++++++++--
1 file changed, 51 insertions(+), 3 deletions(-)
diff --git a/docs/developer/example-depends.md b/docs/developer/example-depends.md
index 5ccb50a42..855597848 100644
--- a/docs/developer/example-depends.md
+++ b/docs/developer/example-depends.md
@@ -26,8 +26,42 @@ You should perform the same steps for [Biopet](https://github.com/biopet/biopet)
### SBT dependencies
-TODO
-
+You can develop biopet pipelines with SBT as well. However, since GATK uses Maven, you will still need to install GATK
+into your local Maven repository with `mvn install`.
+
+After this, you can create a regular `build.sbt` file in the project root directory. In addition to the regular
+SBT settings, you will also need to make SBT aware of the local GATK Maven installation you just did. This can be done
+by adding a new resolver object:
+
+```
+resolvers += {
+ val repo = new IBiblioResolver
+ repo.setM2compatible(true)
+ repo.setName("localhost")
+ repo.setRoot(s"file://${Path.userHome.absolutePath}/.m2/repository")
+ repo.setCheckconsistency(false)
+ new RawRepository(repo)
+}
+```
+
+Having set this, you can then add specific biopet modules as your library dependency. Here is one example that adds
+the Flexiprep version 0.7.0 dependency:
+
+```
+libraryDependencies ++= Seq(
+ "nl.lumc.sasc" % "Flexiprep" % "0.7.0"
+)
+```
+
+In some cases, there may be a conflict with the `org.reflections` package used (this is a transitive dependency of
+GATK). If you encounter this, we recommend forcing the version to 0.9.9-RC1 like so:
+
+```
+libraryDependencies ++= Seq(
+ "org.reflections" % "reflections" % "0.9.9-RC1" force()
+)
+```
+
## Project structure
You should follow typical Scala folder structure. Ideally your IDE will handles this for you.
@@ -99,7 +133,21 @@ For a complete example pom.xml see [here](../examples/pom.xml).
## SBT build
-(skip this section if using Maven)
+You can use SBT to build a fat JAR that contains all the required class files in a single JAR file. This can be done
+using the [sbt-assembly plugin](https://github.com/sbt/sbt-assembly). Keep in mind that you have to explicitly define a specific merge strategy for conflicting
+file names. In our experience, the merge strategy below works quite well:
+
+```
+assemblyMergeStrategy in assembly := {
+ case "git.properties" => MergeStrategy.first
+ // Discard the GATK's queueJobReport.R and use the one from Biopet
+ case PathList("org", "broadinstitute", "gatk", "queue", "util", x) if x.endsWith("queueJobReport.R")
+ => MergeStrategy.first
+ case "GATKText.properties" => MergeStrategy.first
+ case "dependency_list.txt" => MergeStrategy.discard
+ case other => MergeStrategy.defaultMergeStrategy(other)
+}
+```
TODO
--
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