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Minimera

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-. ,-.   ,-. ,-.   .-┃┃┃ ┃ ┃┗┫ ┃,-. ,-.   ,-. ,-.   .-
  \   \ /   \   \ /  ╹ ╹ ┻ ╹ ╹ ┻   \   \ /   \   \ /
 / \   \   / \   \   ┏┳┓┏━╸┏━┓┏━┓ / \   \   / \   \
´   `-´ `-´   `-´ `-´┃┃┃┣╸ ┣┳┛┣━┫´   `-´ `-´   `-´ `-´
                     ╹ ╹┗━╸╹┗╸╹ ╹

Check the man page for information about the command-line minimera interface.

Installation

We provide releases of Minimera as binaries (Linux AMD64 only) and Singularity containers.

Changelog

v0.4.0

Initial beta version. Still under development, things may change.

Building

If you just want to use Minimera you don't need to build it from scratch. You can grab the latest binary or Singularity container from the releases page and don't need to worry about any of this.

If you want to build Minimera from scratch (e.g. to modify it), here are some rough notes to get you started. You should be at least a little familiar with Common Lisp or it's going to be pretty confusing, sorry. You'll need at least:

  • SBCL
  • Quicklisp
  • Buildapp

You'll also need to clone a few projects that aren't in Quicklisp into your Quickload local-projects directory (I'll try to eventually get them into Quicklisp some day, sorry for the fiddliness in the mean time):

  • cl-losh
  • conserve
  • faster

Make sure you can (ql:quickload :minimera) successfully. Then you should be able to run make to:

  1. Generate the ASDF manifest.
  2. Build a minimera binary without Quicklisp by using buildapp with that manifest.
  3. Build a minimera.1 man page.

Tests

There's a (very small) Cram test suite, mostly so I can to avoid breaking things inadvertently before a release. Once you've got cram installed make test to run it.

About

Tool to detect foldback chimeras in Oxford Nanopore data using minimizers.

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