Annotation directory contains development related to annotation side of the service.
Assembly directory contains development related to assembly side of the service.
- Clone and install GAAS
To use the tools in this repository, clone the directory and run make install to update some paths:
git clone https://github.com/NBISweden/GAAS.git
cd GAAS
- A.1) Updates paths in the environment profiles to point to the correct GAAS repository location
make install
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A.2) Dependencies
- You might check that all dependencies are filled up. Depending the scripts you want to use, all dependencies are not required.
make check-
Install the missing perl dependencies
-
With cpanm
cpanm bioperl cpanm Clone cpanm Moose cpanm Graph::Directed cpanm LWP::UserAgent cpanm Statistics::R cpanm JSON cpanm Sort::Naturally cpanm Bio::DB::EUtilities -
With conda
conda env create -f gaas_environment.yml
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-
A.3) Load the correct profiles (add NBIS libs and tools to the PATH)
Three profiles are available to setup the necessary environment variables to use the scripts:- By default:
source profiles/activate_env- If you are on Rackham:
source profiles/activate_rackham_env- If you are on NBIS's servers:
source profiles/activate_nbis_env -
A.4) To get out of the nbis environment and restore your previous environment type
deactivate
-
B.1) Dependencies
-
You might check that all dependencies are filled up. Depending the scripts you want to use, all dependencies are not required.
make check -
Install the missing perl dependencies
- With cpanm
cpanm bioperl cpanm Clone cpanm Moose cpanm Graph::Directed cpanm LWP::UserAgent cpanm Statistics::R cpanm JSON cpanm Sort::Naturally cpanm Bio::DB::EUtilities- With conda
conda env create -f conda_env.yml
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-
B.2) Add the path to the NBIS perl library as well as the bin folder containing all tools. You can add in you ~/.bashrc or ~/.profile file.
export PERL5LIB=$PERL5LIB:/pathTo/GAAS/annotation export PATH=${PATH}:/pathTo/GAAS/annotation/Tools/bin