Commit 839c80aa authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Version cleanup, point all to version 0.5.0

parent d6142527
......@@ -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
......
......@@ -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`:
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......@@ -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
~~~
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......@@ -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
~~~
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......@@ -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
~~~
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......@@ -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)
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......@@ -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]
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