Virtualbox requirements

[satra]

@mjtravers @yarikoptic - add as necessary

• desktop interface/x11
• docker
• singularity 2.5.1

wonder if the following should be installed or done through containers as well

• git
• vi, emacs, pico, nano, gedit

[mjtravers]

@satra - Whew. Thanks! :)

@satra @djarecka Both of you are on Mac? Did you install Docker via "Docker for Mac" or "Docker Toolbox"? I've been digging into Docker's use of its own VirtualBox as a possible cause to the Docker/Singularity problem and was wondering how Docker was installed on your systems.

https://docs.docker.com/docker-for-mac/docker-toolbox/

One tidbit that caught my eye was: "Docker for Mac uses HyperKit instead of Virtual Box."

[djarecka]

@mjtravers - we both have Mac and we both have Docker for Mac

[mjtravers]

@djarecka Ah, okay. Does not seem relevant then.

[djarecka]

@mjtravers - i restarted, removed all data from docker, and it's been working for the last 15min. So maybe it was just a coincidence, but don't remember having this problem with Docker...

[satra]

@mjtravers - finally tracked this down:

https://github.com/kaczmarj/neurodocker/issues/180

we will fix this in the container. but let's install dos2unix (just in case :) )

[mjtravers]

@satra Will make sure dos2unix is in the VM. Wow, that took some serious digging to locate

[jbpoline]

sorry I'm seeing this only now - I think any version above these would be fine - I just need to test my notebook but very confident there will be no issues .. cheers JB

On Mon, Jun 4, 2018 at 1:43 PM, Matt Travers notifications@github.com wrote:

@satra https://github.com/satra @jbpoline https://github.com/jbpoline JB's requirements.txt file has versions attached to the packages which are putting some constraints on the install, which is why I started working with Miniconda. For example, ipython 6.1.0 requires python >= 3.3. Virtualenv (from what I can tell so far, not very familiar with it) will need the additional python version installed in the VM system outside venv and alongside the existing python 2.7. Miniconda handles additional python versions within the conda environments themselves which is a lot easier to manage and does not require the system installation of new python versions. The Miniconda baseline footprint doesn't appear to be very large. Are you thinking of the full Anaconda environment? Here are the baseline packages installed by Miniconda for a new environment:

-

certifi: 2016.2.28-py36_0

-

openssl: 1.0.2l-0

-

pip: 9.0.1-py36_1

-

python: 3.6.2-0

-

readline: 6.2-2

-

setuptools: 36.4.0-py36_1

-

sqlite: 3.13.0-0

-

tk: 8.5.18-0

-

wheel: 0.29.0-py36_0

-

xz: 5.2.3-0

-

zlib: 1.2.11-0

Another way to approach the problem is: JB, how attached are you to the versions specified in your requirements.txt file? Could we simply pull all the versions that work with Python 2.7?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/ReproNim/ohbm2018-training/issues/12#issuecomment-394439345, or mute the thread https://github.com/notifications/unsubscribe-auth/AAQyaMwSo6QBKuPlqZ1kPnqv2r0dN3qcks5t5XHbgaJpZM4UK5DX .

[satra]

closing in favor of #15