You can directly download/clone the repo to use the scripts directly.
$ git clone https://github.com/formbio/laava.git
You can install the dependencies on your own or use one of the following options.
The conda (or mamba) channels and dependencies are in the configuration file laava.conda_env.yml
.
First, install conda via Miniconda or Anaconda. Then, for example, suppose you have anaconda installed and the binary is in $HOME/anaCogentPy37/bin
. To make the installed scripts available in your environment, you would add the binary to $PATH if it isn't there already:
$ export PATH=$HOME/anaCogentPy37/bin:$PATH
Next, use the YAML configuration file to create a new conda environment called laava
and install dependencies:
$ conda env create -f laava.conda_env.yml
Finally, once installation completes, activate the new environment:
$ source activate laava
At this point the prompt should change to (laava) $
and the executable scripts should be available in your PATH.
The Dockerfile
in this repo installs the scripts and all their dependencies into a Docker container image that you can then use to run the scripts.
To build the container image with the name laava
(you can use another name if you prefer):
docker build -t laava:latest -f Dockerfile .
To run the container in the current working directory:
docker run -v $(pwd):$(pwd) -w $(pwd) -it laava:latest bash
This opens a Bash shell with the scripts in the PATH, and the original working directory mounted in place.
The prerequisites to run these scripts include:
- Python 3.7 or later
- R 3.6 or later
Python packages:
R packages:
- tidyverse
- flextable
- Rmarkdown
The test/
subdirectory in this repo contains a Makefile that can fetch example PacBio datasets from a public server and run the scripts on them to reanalyze them and produce example HTML and PDF reports.
Once you've completed installation (above), activate your conda environment or Docker container and change to the test directory:
cd test
To fetch the public datasets and run the complete analysis (this takes some time):
make slow
Or, to just generate the HTML and PDF reports from the existing intermediate files (this takes about 2 minutes):
make fast
Please read the AAV tutorial