Dark matter
Python tools for bioinformatics.
Installation
On Linux (at least) you will need to first:
sudo apt install zlib1g-dev libbz2-dev liblzma-dev
Then you should be able to install via
$ pip install dark-matter
Some additional information is available for Linux, OS X, and Windows.
Optional dependencies
Not all of the following are mandatory. It depends which part of the dark-matter code you try to use.
Picard
run-bowtie2.py can use Picard
to mark duplicates.
GATK
run-bowtie2.py uses gatk if you call
it with --markDuplicatesGATK or --callHaplotypesGATK. If you want to do
this you'll need to download the gatk zip file, unzip it, and either put
the directory where you unzip it into your shell's path or else move the
contents of the zip file into a directory already in your path.
bcftools
You'll need
bcftools if you
want to make consensuses using the make-consensus.py script. Either
follow
the installation instructions
or, if you use brew (or Linux brew), brew install bcftools.
samtools
The run-bowtie2.py and run-bwa.py scripts both make use of
samtools.
EMBOSS
The compare-sequences.py script (if called with --align) requires the
needle and (possibly) stretcher from
EMBOSS.
iPython Notebook
If you are using dark matter in an
iPython Notebook, you should install
the requirements in requirements-ipynb.txt.
DIAMOND
If you want to use the DIAMOND functionality of
dark-matter you will need DIAMOND version 2.1.16 or newer installed.
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