- Pull the image from DockerHub
docker pull macmaneslab/orp:2.3.3
\2. Alternatively, but probably not preferred, to build the image from scratch.
docker build -t orp:2.3.3 -f $HOME/Oyster_River_Protocol/Dockerfile/Dockerfile .
\3. Run the Image
docker run -it macmaneslab/orp:2.3.3 bash
#or with adding a drive, changing `/home/ubuntu/` to your mountpoint
docker run -it \
--mount type=bind,source=/home/ubuntu/,target=/home/orp/docker \
macmaneslab/orp:2.3.3 bash
\4. Test the Installation
cd $HOME/Oyster_River_Protocol/sampledata
conda activate orp
$HOME/Oyster_River_Protocol/oyster.mk \
STRAND=RF \
TPM_FILT=1 \
MEM=5 \
CPU=4 \
READ1=test.1.fq.gz \
READ2=test.2.fq.gz \
RUNOUT=test