USAGE.txt

USAGE

The simplest way to start using this image is to make yourself
a script and run docker from there.  See examples below.

You would run it something like:

  bash runAT.bash "tleap -f tleap.input"


For non-interactive utilities, e.g., sander, try a
    script like the following.  

    This one also handles utilities that need a username,
    for example OpenMPI.
=======================================================
=========== run_AT.bash NON-interactive ===============
=======================================================
#!/bin/bash

## bash file for running an amber utility that 
## does not expect an interactive session, e.g., sander

##
## Change these variables as desired
IMAGE='ambertools:16'
#IMAGE='lachele/ambertools:16'
WORKDIR=$(pwd) # use an absolute path if you change this
GROUP=${GROUPS[0]}  # your group id
RM='true'  # change to false to keep the container around
           # after you have used it
           # ...this is generally not desirable
##
##
docker run --rm=${RM} \
  -v ${WORKDIR}:/home/working \
  ${IMAGE} \
  /bin/bash -c "\
  chown $UID:${GROUP} /home/working \
  && groupadd -g ${GROUP} working \
  && adduser --home /home/working \
      --shell /bin/bash \
      --uid $UID \
      --gid ${GROUP} \
      --disabled-password \
      --system working \
  && su - working \
  && cd /home/working \
  && source /usr/local/amber16/amber.sh \
  &&  $1"
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For interactive utilities, e.g., tleap, try a
    script like the following.  This one won't work 
    well with utilities that want a username. 
=======================================================
============ run_iAT.bash Interactive =================
=======================================================
#!/bin/bash

## bash file for running an amber utility that 
## expects an interactive session, e.g., tleap

##
## Change these variables as desired
IMAGE='ambertools:16'
#IMAGE='lachele/ambertools:16'
WORKDIR=$(pwd) # use an absolute path if you change this
USER=$UID  # your user id
GROUP=${GROUPS[0]}  # your group id
RM='true'  # change to false to keep the container around
           # after you have used it
           # ...this is generally not desirable
##
##

docker run -it --rm=${RM} \
  -v ${WORKDIR}:/home/working \
  -u="${USER}:${GROUP}" \
  -w="/home/working" \
  ${IMAGE} \
  /bin/bash -c "source /usr/local/amber16/amber.sh \
  && $1"
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