Getting started

Installing

Trying to install bioinformatics software can often lead to headaches, so I’ve dedicated a lot of time to making MiniContourFinder easy to install regardless of operating system. However, installing and using MiniContourFinder requires basic knowledge of the command line and either of the common package manager pip or conda.

`pip` install

Currently, the easiest way to install MiniContourFinder is with pip. Chances are that you already have pip installed because it comes prepackaged with Python (at least since v3.4/v2.7.9). To check if pip is installed, open up a terminal and check if the following outputs look similar.

$ python --version
Python 3.N.N
$ python -m pip --version
pip X.Y.Y from ... (python 3.N.N)

If your default version of Python is 2.N.N instead of 3.N.N, try the same commands, but with python3 instead of python, and pip3 instead of pip. If that didn’t work, follow the installation guide here.

If it did, you can now install MiniContourFinder simply by running

$ pip install MiniContourFinder

It will produce an output detailing the requirements that were already satisfied and that were missing (and installed along with MiniContourFinder)

Collecting MiniContourFinder
  Downloading MiniContourFinder-1.0.14-py3-none-any.whl (47 kB)
    |████████████████████████████████| 47 kB 3.9 MB/s
...
Installing collected packages: MiniContourFinder...

Successfully installed MiniContourFinder-1.0.14...

Attention

ModuleNotFoundError: No module named 'Image'

There are well documented problems installing the module Image from PIL, pillow, or Pillow. If pip begins to install MiniContourFinder, but it exits with a ModuleNotFoundError that looks similar to

ModuleNotFoundError: No module named 'Image'
----------------------------------------
ERROR: Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output.

then you’ll have to install Pillow yourself with pip before installing MiniContourFinder.

$ pip install Pillow
$ pip install MiniContourFinder

Conda install

I’ve also published MiniContourFinder on Anaconda, here, but the install isn’t functional yet. In the future, conda will be the prefered installation platform. To check if conda is already installed, you can enter conda info in a terminal, which should print information about your installation.

If conda is not installed, you can install it easily through a download, here, or use the command line, which I prefer and outline below. conda comes in either Anaconda, or Miniconda; the difference between the two being that Anaconda comes with loads of things preinstalled, while Miniconda is more bare bones. I prefer Miniconder, and will show an example macOS install below, but you read more about the differences here.

First, copy the repsective 64-bit install link from the conda docs for your operating system (note that for macOS you want the “bash”, not “pkg” version). Open a terminal and run

$ curl -O https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh

That’s a capital “o”, not a zero. This will download the installer. Next, run the installed with

$ bash Miniconda3-latest-MacOSX-x86_64.sh

After following all the prompts and reading the license you should have conda installed! The last thing to do is “restart” your terminal so that is recognizes conda. This can be done by quiting and reopening your terminal, or with the following

$ source ~/.bash_profile

Now when you type conda info in your terminal you should return the installation info.

GitHub install

MiniContourFinder can be installed by cloning the GitHub repo.

$ git clone https://github.com/isgilman/MiniContourFinder
$ cd MiniContourFinder
$ python setup.py install

Verifying your installation

I haven’t gotten around to writing install tests yet, but you can check to see that your install is working by typing

$ mcf -h

which should bring up the help info.

Uninstalling

Uninstalling with `pip`

Uninstalling with pip is just as easy. My version lives in a directory called junkdrawer.

$ pip uninstall MiniContourFinder
Found existing installation: MiniContourFinder 1.0.14
Uninstalling MiniContourFinder-1.0.14:
  Would remove:
    junkdrawer/bin/mcf
    junkdrawer/bin/mcf_gui
    junkdrawer/bin/mcf_parallel
    junkdrawer/lib/python3.8/site-packages/MCF/*
    junkdrawer/lib/python3.8/site-packages/MiniContourFinder-1.0.14.dist-info/*

Then enter y or Y at the prompt.

Proceed (Y/n)? y
  Successfully uninstalled MiniContourFinder-1.0.14

Uninstalling with `conda`

Uninstalling GitHub install

If you installed MiniContourFinder from the GitHub repo, you can uninstall it with pip, as above.

$ pip uninstall MiniContourFinder

After that finished, navigate to the directory you downloaded the repo to, and delete it. My installation lives in junkdrawer.

$ cd junkdrawer
$ rm -r MiniContourFinder