Commit e17daab5 authored by Sander Bollen's avatar Sander Bollen
Browse files

Merge branch 'fix-vep_versions' into 'develop'

Fixed lazy val



See merge request !495
parents 5cf8b675 ecd019f6
......@@ -30,6 +30,12 @@ import scala.io.Source
*/
class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFunction with Reference with Version with Summarizable {
lazy val vepVersion = new LazyCheck({
val s: Option[String] = config("vep_version")
s
})
vepVersion()
executable = config("exe", namespace = "perl", default = "perl")
var vepScript: String = config("vep_script")
......@@ -39,13 +45,8 @@ class VariantEffectPredictor(val root: Configurable) extends BiopetCommandLineFu
@Output(doc = "output file", required = true)
var output: File = null
lazy val vepConfig = new LazyCheck({
val s: Option[String] = config("vep_config")
s
})
override def subPath = {
if (vepConfig.isSet) super.subPath ++ vepConfig()
if (vepVersion.isSet) super.subPath ++ List("vep_settings") ++ vepVersion()
else super.subPath
}
......
......@@ -55,6 +55,27 @@ With that in mind, an example configuration using mode `standard` of the VepNorm
}
~~~
Multiple global configurations
------------------------------
It's possible to make a global config with multiple version of cache / vep in there. This way a user only needs to supply the `vep_version` config value.
Gloabl config:
``` yaml
vep_settings:
86:
vep_script: <path_to_exe>
dir: <path_to_cache>
75:
vep_script: <path_to_exe>
dir: <path_to_cache>
```
User config:
``` yaml
vep_version: 75 or 86
```
Varda
-----
Annotation with a [Varda](http://varda.readthedocs.org/en/latest/) database instance is possible.
......
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