Installing dnaapler
dnaapler
requires only BLAST v2.9 or higher as an external dependency.
The easiest way to install dnaapler is via conda. This method is highly recommended, because this will install BLAST automatically.
If you need instructions on how to install conda, please see the end of this page.
Conda
dnaapler
is available on bioconda.
conda install -c bioconda dnaapler
Pip
You can also install dnaapler
with pip.
pip install dnaapler
If you install dnaapler
with pip, then you will then need to install BLAST v 2.9 or higher separately. It will need to be available in the $PATH
or else dnaapler
will not work.
Beginner Conda Installation
If you are new to using the command-line, please install conda using the following instructions.
First install Anaconda. There are lots of options but the two best in our opinion are:
Please follow the instructions at the links to install based on your computer architecture.
- Note: We would recommend install miniforge as it will automatically install mamba, which is much faster than base conda.
After your installation is complete, you should add the following channels to your conda configuration:
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
We would recommend installing dnaapler into a fresh environment. Assuming you installed miniforge, to create a environment called dnaaplerENV with dnaapler installed:
- To create a conda environment called
dnaapler_env
conda create -n dnaapler_env
- To activate the environment
conda activate dnaapler_env
- To install dnaapler
mamba install -c bioconda dnaapler
- Once that has finished downloading and installing, you can check installation worked using:
dnaapler -h
- You should see:
Usage: dnaapler [OPTIONS] COMMAND [ARGS]...
Options:
-h, --help Show this message and exit.
-V, --version Show the version and exit.
Commands:
all Reorients contigs to begin with any of dnaA, repA or terL
bulk Reorients multiple genomes to begin with the same gene
chromosome Reorients your genome to begin with the dnaA chromosomal...
citation Print the citation(s) for this tool
custom Reorients your genome with a custom database
largest Reorients your genome the begin with the largest CDS as...
mystery Reorients your genome with a random CDS
nearest Reorients your genome the begin with the first CDS as...
phage Reorients your genome to begin with the terL large...
plasmid Reorients your genome to begin with the repA replication...