Version cleanup, point all to version 0.5.0

docs/general/about.md

@@ -15,7 +15,7 @@ need.
 
 ## Contributors
 
-As of the 0.4.0 release, the following people (sorted by last name) have contributed to Biopet:
+As of the 0.5.0 release, the following people (sorted by last name) have contributed to Biopet:
 
 - Wibowo Arindrarto
 - Sander Bollen

docs/index.md

@@ -13,10 +13,10 @@ Biopet (Bio Pipeline Execution Toolkit) is the main pipeline development framewo
 Biopet is available as a JAR package in SHARK. The easiest way to start using it is to activate the `biopet` environment module, which sets useful aliases and environment variables:
 
 ~~~
-$ module load biopet/v0.4.0
+$ module load biopet/v0.5.0
 ~~~
 
-With each Biopet release, an accompanying environment module is also released. The latest release is version 0.4.0, thus `biopet/v0.4.0` is the module you would want to load.
+With each Biopet release, an accompanying environment module is also released. The latest release is version 0.5.0, thus `biopet/v0.5.0` is the module you would want to load.
 
 After loading the module, you can access the biopet package by simply typing `biopet`:
 

docs/pipelines/bam2wig.md

@@ -33,7 +33,7 @@ Arguments for Bam2Wig:
 If you are on SHARK, you can also load the `biopet` module and execute `biopet pipeline` instead:
 
 ~~~bash
-$ module load biopet/v0.3.0
+$ module load biopet/v0.5.0
 $ biopet pipeline bam2wig
 
 ~~~

docs/pipelines/gentrap.md

@@ -125,7 +125,7 @@ $ java -jar </path/to/biopet.jar> pipeline gentrap -config </path/to/config.json
 You can also use the `biopet` environment module (recommended) when you are running the pipeline in SHARK:
 
 ~~~
-$ module load biopet/v0.3.1
+$ module load biopet/v0.5.0
 $ biopet pipeline gentrap -config </path/to/config.json> -qsub -jobParaEnv BWA -run
 ~~~
 

docs/pipelines/sage.md

@@ -49,7 +49,7 @@ Arguments for Sage:
 If you are on SHARK, you can also load the `biopet` module and execute `biopet pipeline` instead:
 
 ~~~
-$ module load biopet/v0.3.0
+$ module load biopet/v0.5.0
 $ biopet pipeline sage
 
 ~~~

docs/pipelines/toucan.md

@@ -12,7 +12,7 @@ Currently, it comprises just two steps:
 Example
 -----------
 ~~~~bash
-java -jar Biopet-0.3.0.jar pipeline Toucan -h
+biopet pipeline Toucan -h
 Arguments for Toucan:
  -Input,--inputvcf <inputvcf>          Input VCF file
  -config,--config_file <config_file>   JSON config file(s)

docs/tools/VepNormalizer.md

@@ -22,7 +22,7 @@ Example
 ---------
 
 ~~~~bash
-java -jar Biopet-0.3.0.jar tool VepNormalizer -h
+biopet tool VepNormalizer -h
 |VepNormalizer - Parse VEP-annotated VCF to standard VCF format 
 Usage: VepNormalizer [options]