GAAS
Genome Assembly Annotation Service (GAAS)
Suite of tools related to Genome Assembly Annotation Service tasks.
Table of Contents
What can GAAS do for you?
The repository contains mainly tools and knowledge related to bioinformatics and annotation the most often. To access and install the tools please follow the installation procedures below. For the knowledge you are invited to visit the knowledge part of the repo or if you are looking specifically for genome assembly knowledge The Genome Assembly Workshop Knowledge Base.
Installation
Using conda
Install
conda install -c bioconda gaas
Update
conda update gaas
Uninstall
conda uninstall gaas
Old school
Prerequisites
-
R
-
Perl Perl >= 5.8, and a list of perl modules that can be installed using cpan, cpanm or conda:
- Install perl modules with cpanm
cpanm install bioperl cpanm install Clone cpanm install Graph::Directed cpanm install LWP::UserAgent cpanm install Statistics::R cpanm install Sort::Naturally cpanm install File::Share cpanm install Moose cpanm install File::ShareDir::Install cpanm install Bio::DB::EUtilities- Install perl modules with conda
conda env create -f conda_environment_GAAS.yml conda activate gaas
Install
git clone https://github.com/NBISweden/GAAS.git # Clone GAAS
cd GAAS # move into GAAS folder
perl Makefile.PL # Check all the dependencies*
make # Compile
make test # Test
make install # Install
*If dependencies are missing you can install them using cpan/cpanm or use conda and load the environment conda_environment_GAAS.yml
Remark: On MS Windows, instead of make you'd probably have to use dmake or nmake depending the toolchain you have.
Update
From the folder where the repository is located.
git pull # Update to last GAAS
perl Makefile.PL # Check all the dependencies<sup>1</sup>
make # Compile
make test # Test
make install # Install
Change to a specific version
From the folder where the repository is located.
git pull # Update the code
git checkout v0.1.1 # use version v0.1 (See releases tab for a list of available versions)
perl Makefile.PL # Check all the dependencies<sup>1</sup>
make # Compile
make test # Test
make install # Install
Uninstall
perl uninstall_GAAS
Usage
script_name.pl -h
Repository structure
annotation
Annotation directory contains everything related to annotation side of the service.
Shorcuts:
assembly
Assembly directory contains development related to assembly side of the service.