yibing-liu/battenberg

Battenberg R package for subclonal copynumber estimation

Battenberg

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Advised installation and running instructions

Please visit the cgpBattenberg page, download the code from there and run the setup.sh script. The battenberg.pl script can then be used to run the pipeline.

Advanced installation instructions

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.

Standalone

Prerequisites

Installing from Github requires devtools and Battenberg requires readr, RColorBrewer and ASCAT. The pipeline requires doParallel. From the command line run:

R -q -e 'source("http://bioconductor.org/biocLite.R"); biocLite(c("devtools", "readr", "doParallel", "ggplot2", "RColorBrewer", "gridExtra", "gtools"));'
R -q -e 'devtools::install_github("Crick-CancerGenomics/ascat/ASCAT")'

Installation from Github

To install Battenberg, run the following from the command line:

R -q -e 'devtools::install_github("Wedge-Oxford/battenberg")'

Required reference files

Battenberg requires a number of reference files that should be downloaded.

• ftp://ftp.sanger.ac.uk/pub/teams/113/Battenberg/battenberg_1000genomesloci2012_v3.tar.gz
• ftp://ftp.sanger.ac.uk/pub/teams/113/Battenberg/battenberg_impute_1000G_v3.tar.gz
• ftp://ftp.sanger.ac.uk/pub/teams/113/Battenberg/probloci_270415.txt.gz
• ftp://ftp.sanger.ac.uk/pub/teams/113/Battenberg/battenberg_wgs_gc_correction_1000g_v3.tar.gz
• ftp://ftp.sanger.ac.uk/pub/teams/113/Battenberg/battenberg_snp6_exe.tgz (SNP6 only)
• ftp://ftp.sanger.ac.uk/pub/teams/113/Battenberg/battenberg_snp6_ref.tgz (SNP6 only)

Pipeline

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://raw.githubusercontent.com/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.

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

In RStudio: In the Build tab, click Check Package

Then open the NAMESPACE file and edit:

S3method(plot,haplotype.data)

to:

export(plot.haplotype.data)