https://github.com/kdm9/usc-demo
Demo of the userspace containers project at the Common Workflow Language
https://github.com/kdm9/usc-demo
Last synced: about 2 months ago
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Demo of the userspace containers project at the Common Workflow Language
- Host: GitHub
- URL: https://github.com/kdm9/usc-demo
- Owner: kdm9
- License: other
- Created: 2016-02-17T19:27:37.000Z (over 9 years ago)
- Default Branch: master
- Last Pushed: 2016-09-27T05:28:59.000Z (over 8 years ago)
- Last Synced: 2025-02-14T21:46:52.345Z (4 months ago)
- Language: Python
- Homepage:
- Size: 6.34 MB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 1
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
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README
===========================
Userspace Containers PoC[1]
===========================
This is a demonstration of using `proot `_ as a
fully-userspace containerisation platform. Using proot, it is possible to
execute workflows in isolated environments on e.g. HPC clusters:
- as an unprivileged user
- without any setuid binaries
- fully within $HOME or any other writeable directory
- without any admin help or installation
In this repo is a Dockerfile that creates an Debian image within which we can
install khmer.
.. [#] PoC here standing for Proot-of-concept ;)
Demo
^^^^
To run this demo you will need installed on your local computer:
- ``docker``: get it from `docker.com `_
- ``python-docker``: ``pip install docker-py``
- ``python-docopt``: ``pip install docopt``
I refer below to ```` or your remote machine. This could be any
computer running a Linux kernel. Your laptop, your local dev box, your HPC
cluster, your router...
1. Run ``make`` to create a rootfs.tar
2. ``scp rootfs.tar :~/``
3. On your remote machine, do:
.. code-block:: shell
mkdir ~/usc-demo
cd ~/usc-demo
wget -nv -O proot http://portable.proot.me/proot-x86_64
chmod +x ./proot
mkdir -p rootfs
tar xvf ~/rootfs.tar
This will install ``proot`` and set up the rootfs you made locally in step
1.
4. Prove to yourself that your HPC cluster is useless:
.. code-block:: shell
# Unless you're very lucky, the following will fail wherever you normally
# do your computation
apt-get update
apt-get install khmer
5. Run proot to create an isolated environment:
.. code-block:: shell
env -i ./proot -S ./rootfs /bin/bash
# You should now see a prompt ending in '#', indicating you are root
# Now, we will try installing khmer again:
apt-get update
apt-get install khmer
# Whoo! If this hasn't broken your brain, then it was already broken
# Let's hash some reads and calculate and abundance histogram
load-into-counting.py -M 1e8 -k 32 sequence.cg sequence.fasta
abundance-dist.py sequence.cg sequence.fasta hist.csv
cat hist.csv