seq2HLA on BAM files
Authors: Ed Green Date: October 2016 Version: 1.0
Installed Sofware seq2HLA 2.2
docker pull edgreen/seq2hla:latest
To build from the Dockerfile clone the repository using the following command:
Change directory to the downloaded files:
cd Docker_seq2hla
Ensure you have Docker installed (and that you don't need to be sudo to run it) and build the image:
docker build .
If you are behind a proxy server you will need to add these details:
docker build --build-arg HTTPS_PROXY=https://xxx .
Run with the following command, setting inputBAM as your BAM file (i.e. for foo.bam inputBAM=foo)
docker run -it -v /path/to/file/dir/:/workspace/ -e inputBAM=xx -e threadsN edgreen/seq2hla:latest
Remember to use the docker run --rm command if you want to remove the stopped container, otherwise looping over files will take up a lot of disk space!
An example script is provided that iterates over directories and processes the bam files in each
Ed Green
egreen@dkfz-heidelberg.de
DKFZ,
G160,
Im Neuenheimer Feldt 280,
Heidelberg 69120,
Germany