jupyter/minimal-notebook lab-3.4.2 2e23237afba6 16 months ago 1.5GB
FROM jupyter/minimal-notebook:lab-3.4.2
docker build -t test/mysamtools:1.0 .
docker images
apt-get update && apt-get -y install samtools=1.10-3 && apt-get clean
conda install -c bioconda samtools
cd samtools-1.x # after downloading the source code ./configure --prefix=/where/to/install make make install export PATH=/where/to/install/bin:$PATH
USER root RUN apt-get update && apt-get -y install samtools=1.10-3 && apt-get clean
FROM jupyter/minimal-notebook:lab-3.4.2 USER root RUN apt-get update && apt-get -y install samtools=1.10-3 && apt-get clean
docker build -t test/mysamtools:1.0 .
Successfully built 5e6bcf35081d Successfully tagged test/mysamtools:1.0
docker run --rm test/mysamtools:1.0 samtools help
CMD ["samtools"]
docker run --rm test/mysamtools:1.0 # Will run samtools
WORKDIR /data/
docker version
docker --help
docker [OPTIONS] COMMAND [arg...]
docker pull --help
docker pull biocontainers/fastqc Using default tag: latest Error response from daemon: manifest for biocontainers/fastqc:latest not found: manifest unknown: manifest unknown
docker pull biocontainers/fastqc:v0.11.9_cv8
docker pull biocontainers/fastqc:v0.11.9_cv8
docker images
docker inspect biocontainers/fastqc:v0.11.9_cv8
docker run --help
docker run biocontainers/fastqc:v0.11.9_cv8 fastqc --help
docker run --help
pwd
#docker inspect --format='{{.Config.Volumes}}' biocontainers/fastqc:v0.11.9_cv8 docker inspect --format='{{.Config.WorkingDir}}' biocontainers/fastqc:v0.11.9_cv8
docker run biocontainers/fastqc:v0.11.9_cv8 ls /data
docker run -v ${PWD}:/data/ biocontainers/fastqc:v0.11.9_cv8 ls /data/
ls
docker run -v ${PWD}:/data/ biocontainers/fastqc:v0.11.9_cv8 fastqc /data/Data/SRR3105699_chr18.fastq.gz
docker pull quay.io/biocontainers/fastqc:0.11.9--hdfd78af_1