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Installation
vgan is supported for use on Linux systems.
The easiest way to run vgan is to download the static binary.
Step 1: Download the static binary.
The list of releases is here: https://github.com/grenaud/vgan/tags Each release comes with a static binary. Find the URL of the static binary by right-clicking and selecting "copy link"
wget [URL TO RELEASE BINARY]
Where you paste the URL of the binary, copy the executable in a bin/ directory in your home directory:
mkdir -P $HOME/bin/
cp vgan $HOME/bin/
Step 2: Mark the binary executable:
chmod +x $HOME/bin/vgan
Step 3: Create the vgan folder structure:
mkdir -P $HOME/share/vgan/euka_dir/
mkdir -P $HOME/share/vgan/hcfiles/
mkdir -P $HOME/share/vgan/soibean_dir/
mkdir -P $HOME/share/vgan/damageProfiles/
mkdir -P $HOME/share/vgan/plottingScripts/
Once the folder structure is created, we can download the necessary files. Find download instructions for euka, HaploCart, and soibean.
Make sure conda is installed or follow the conda install guide: https://docs.conda.io/projects/conda/en/latest/user-guide/install/index.html. The Bioconda channel must be installed in your environment.
To install vgan, use:
conda install -c bioconda vgan
When using vgan via conda, you also must download the necessary files as described before. You can find detailed instructions for each subcommand in its tab.
Please ensure that git is installed on your system. You can check by typing "git --version".
If you wish to build from source, you will need the build-essential package. If it is not already installed, please run
sudo apt-get install build-essential
You will also need wget. If you do not have it please run
sudo apt-get install wget
vgan requires vg https://github.com/vgteam/vg. vg requires several packages to be installed; please refer to the README in vg.
git clone https://github.com/grenaud/vgan.git
cd vgan/src && make
Please be patient, this will take some time.
If you are building on a WSL subsystem you may receive an error due to VG not building entirely. This is likely to be a permissions issue. Please run the above command as a root user. (i.e. cd vgan/src && sudo make)
If the build has been successful, the executable will be found in the bin folder.
If you build from source, you can download the requisite files for HaploCart with
make hcfilesmade
and for euka:
make eukafilesmade
If euka is to be used by multiple users, please ensure that the file $HOME/share/vgan/euka_dir/euka_db.dist has writing permission with the following command:
sudo chmod +w $HOME/share/vgan/euka_dir/euka_db.dist
from the src directory
and for soibean:
make soibeanfilesmade
vgan requires VG as a dependency. If there are issues with making vg, please see https://github.com/vgteam/vg for further documentation. vg requires several packages to install.