Trick to deploy software securely as a docker image on a production system

Install Docker on the system machine
Pull the image for the software, e.g. Bowtie using the image genomicpariscentre/bowtie1
Create a file /usr/bin/bowtie with the following content:

#! /bin/bash
uid=`id -u $LOGNAME`
gid=`id -g $LOGNAME`
docker run --rm -u $uid:$gid -v $PWD:$PWD -v $HOME:$HOME -w $PWD genomicpariscentre/bowtie1 bowtie ${@:1}

Create a file /etc/sudoers.d/bowtie with the following content:

%users      ALL=(ALL) NOPASSWD: /usr/bin/bowtie

Now any user can run Bowtie using password-less sudo:

[user@host]$ sudo bowtie --version
bowtie version 1.1.1
64-bit
Built on fbc229a23508
Wed Mar 25 10:58:01 UTC 2015
Compiler: gcc version 4.6.3 (Ubuntu/Linaro 4.6.3-1ubuntu5)
Options: -O3 -m64  -Wl,--hash-style=both -DPOPCNT_CAPABILITY -static -static
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}