8000 GitHub - formbio/laava at v2.5
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

formbio/laava

Repository files navigation

LAAVA: Long-read AAV Analysis

Installation

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.

Option 1: Conda

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.

Option 2: Docker

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.

Option 3: Manual installation

The prerequisites to run these scripts include:

  • Python 3.7 or later
  • R 3.6 or later

Python packages:

R packages:

  • tidyverse
  • flextable
  • Rmarkdown

Testing

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

Usage

Please read the AAV tutorial

About

LAAVA: Long-read AAV Analysis

Resources

License

Stars

Watchers

Forks

Packages

 
 
 

Contributors 6

0