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Installation#

Using Docker#

First you must have Docker installed and running.
Secondly have look at the availabe AGAT biocontainers at quay.io.

Then: 

# get the chosen AGAT container version
docker pull quay.io/biocontainers/agat:0.8.0--pl5262hdfd78af_0
# use an AGAT's tool e.g. agat_convert_sp_gxf2gxf.pl
docker run quay.io/biocontainers/agat:0.8.0--pl5262hdfd78af_0 agat_convert_sp_gxf2gxf.pl --help

Using Singularity#

First you must have Singularity installed and running.
Secondly have look at the availabe AGAT biocontainers at quay.io.

Then: 

# get the chosen AGAT container version
singularity pull docker://quay.io/biocontainers/agat:1.0.0--pl5321hdfd78af_0
# run the container
singularity run agat_1.0.0--pl5321hdfd78af_0.sif

You are now in the container. You can use an AGAT's tool e.g. agat_convert_sp_gxf2gxf.pl doing 

agat_convert_sp_gxf2gxf.pl --help

Using Bioconda#

Install AGAT#

conda install -c bioconda agat

or in a fresh environment:

conda create -c bioconda -n agat agat

Update AGAT#

conda update agat

Uninstall AGAT#

conda uninstall agat

Old school - Manually#

You will have to install all prerequisites and AGAT manually.

Install prerequisites#

  • R (optional)
    You can install it by conda (conda install r-base), through CRAN (See here for a nice tutorial) or using your package management tool (e.g apt for Debian, Ubuntu, and related Linux distributions). R is optional and can be used to perform some plots. You will need to install the perl depency Statistics::R

  • Perl >= 5.8
    It should already be available on your computer. If you are unlucky perl.org is the place to go.

  • Perl modules
    They can be installed in different ways:

    • using cpan or cpanm
    cpanm install bioperl Clone Graph::Directed LWP::UserAgent Carp Sort::Naturally File::Share File::ShareDir::Install Moose YAML LWP::Protocol::https Term::ProgressBar

    • using conda

    • using the provided yaml file

    conda env create -f conda_environment_AGAT.yml
conda activate agat
    • manually 
    conda install perl-bioperl perl-clone perl-graph perl-lwp-simple perl-carp perl-sort-naturally perl-file-share perl-file-sharedir-install perl-moose perl-yaml perl-lwp-protocol-https perl-term-progressbar
    • using your package management tool (e.g apt for Debian, Ubuntu, and related Linux distributions)
    apt install libbio-perl-perl libclone-perl libgraph-perl liblwp-useragent-determined-perl libstatistics-r-perl libcarp-clan-perl libsort-naturally-perl libfile-share-perl libfile-sharedir libfile-sharedir-install-perl libyaml-perl liblwp-protocol-https-perl libterm-progressbar-perl

  • Optional Some scripts offer the possibility to perform plots. You will need R and Statistics::R which are not included by default.

    • R
      You can install it by conda (conda install r-base), through CRAN (See here for a nice tutorial) or using your package management tool (e.g apt for Debian, Ubuntu, and related Linux distributions).

    • Statistics::R You can install it through conda (conda install perl-statistics-r), using cpan/cpanm (cpanm install Statistics::R), or your package management tool (apt install libstatistics-r-perl)

Install AGAT#

git clone https://github.com/NBISweden/AGAT.git # Clone AGAT
cd AGAT                                         # move into AGAT folder
perl Makefile.PL                                # Check all the dependencies*
make                                            # Compile
make test                                       # Test
make install                                    # Install

*If dependencies are missing you will be warn. Please refer to the Install prerequisites section.

Remark: On MS Windows, instead of make you'd probably have to use dmake or nmake depending the toolchain you have.

Update AGAT#

From the folder where the repository is located.

git pull                                        # Update to last AGAT
perl Makefile.PL                                # Check all the dependencies*
make                                            # Compile
make test                                       # Test
make install                                    # Install
*If dependencies are missing you will be warn. Please refer to the Install prerequisites section.

Change to a specific version#

From the folder where the repository is located. 

git pull                                        # Update the code
git checkout v0.1                               # use version v0.1 (See releases tab for a list of available versions)
perl Makefile.PL                                # Check all the dependencies*
make                                            # Compile
make test                                       # Test
make install                                    # Install
*If dependencies are missing you will be warn. Please refer to the Install prerequisites section.

Uninstall AGAT#

perl uninstall_AGAT