PacBio SMRT Analysis Server in Docker

Dockerfile

FROM centos

# following http://www.pacb.com/wp-content/uploads/2015/09/SMRT-Analysis-Software-Installation-v2.3.0.pdf

MAINTAINER [email protected]

ENV SMRT_ROOT=/opt/smrtanalysis/
ENV SMRT_USER=smrtanalysis
ENV SMRT_GROUP=smrtanalysis

RUN yum groupinstall -y "Development Tools"
RUN yum install -y redhat-lsb net-tools

RUN groupadd $SMRT_GROUP
RUN adduser \
  --gid $SMRT_GROUP \
  --home-dir $SMRT_ROOT \
  --create-home \
  --shell /bin/bash \
  $SMRT_USER

USER $SMRT_USER
WORKDIR $SMRT_ROOT

RUN curl -LO -# \
  http://files.pacb.com/software/smrtanalysis/2.3.0/smrtanalysis_2.3.0.140936.run

RUN curl -LO -# \
  https://s3.amazonaws.com/files.pacb.com/software/smrtanalysis/2.3.0/smrtanalysis-patch_2.3.0.140936.p5.run

RUN bash \
  smrtanalysis_2.3.0.140936.run \
  -p smrtanalysis-patch_2.3.0.140936.p5.run \
  --rootdir $SMRT_ROOT \
  --batch \
  --ignore-syscheck \
  --jmstype NONE

ADD ./run .

EXPOSE 8080

ENTRYPOINT ["./run"]

run

set -euo pipefail

# runs as daemon in background
${SMRT_ROOT}/admin/bin/smrtportald-initd start

# sleep forever to prevent container from exiting
while sleep 1000; do
  echo "hello"
done

Hi,
I tried to use your Dockerfile in the following way docker run -d --net=host --privileged=true -v /mnt/data:/export sort, but received docker: Error response from daemon: Container command './run' could not be invoked..

However, the Dockerfile and the run script are both in the same folder and when I built the container run was added successfully to the container:

Step 15 : ADD ./run .
 ---> f6972313a004
Removing intermediate container 24d92f7e81df
Step 16 : EXPOSE 8080
 ---> Running in ee6f9345a3c5
 ---> 6dc9d4ca0d61
Removing intermediate container ee6f9345a3c5
Step 17 : ENTRYPOINT ./run
 ---> Running in a3243dae9c82
 ---> 2bde541f1c91
Removing intermediate container a3243dae9c82
Successfully built 2bde541f1c91

What did I do wrong?

Thank you in advance.

Mic