Download & Install

Binary distributions are available for Linux and OS.X.

Download Linux Download OS.X

GitHub

Install

Uncompress the binary at your HOME directory

cd 
tar -xvzf path/to/bds*.tar.gz

Requirements: In order to run bds, you need Java 1.11.

Note: bds's directoy .bds is 'hidden', since the name starts with a dot. Add bds's directory to your PATH, by adding the following line to your .bashrc or .bash_profile

export PATH=$PATH:$HOME/.bds

Installing from source

The source code is available at GitHub, here we show how to compile and install.

Requirements: In order to complile bds, you need

  • Java version 12 or higher
  • Go version 1.0 or higher
  • Ant version 1.7 or higher
  • Maven version 3.8 or higher

The source code is available on Github. Download the project as follows:

# Clone repository
$ git clone https://github.com/pcingola/bds.git

Once you downloaded the project, you can install using the install.sh script:

# Run 'install script
cd bds
./scripts/install.sh

Then you should add bds to your PATH. Edit your .bashrc (or .bash_profile) and add the following lines

# bds
export PATH=$PATH:$HOME/.bds/

Optional: If you have root access, you can do the following (to get bds available everywhere in your system)

su -
cd /usr/bin/
ln -s /home/your_user/.bds/bds

Build Jar: Solving missing Java libraries

These are used to build the JAR file

Build executable jar with dependencies

Jar with dependencies in directory 'target', e.g. target/bds-2.3-jar-with-dependencies.jar

cd mvn
mvn clean assembly:assembly

Copy depdencies

Libraries are copied to: target/dependency

cd mvn
mvn dependency:copy-dependencies

Creating manual pages

Maual pages are written in Markdown (*.md) and HTML is created using mkdocs package. The source Markdown documents are located in manual/docs/.

The GitHub pages are published from master branch, direcotory /docs, so manual pages are created in a sub-directory (docs/manual/site)

Create a virtual environment for mkdocs

mkdir $HOME/bds_docs
cd $HOME/bds_docs
virtualenv -p python3 .

# Activate virtualenv and install mkdocs
. bin/activate
pip install mkdocs

# Create links to bds project.
# Here we assume the source code is at `$HOME/workspace/bds`
BDS_SRC="$HOME/workspace/bds"
ln -s $BDS_SRC/manual/mkdocs.yml  # Main configuration file for mkdocs
ln -s $BDS_SRC/manual/docs        # Source markdown for manual pages
ln -s $BDS_SRC/docs/manual/site   # GitHub pages are in 'docs' directory

Once the virtual environment for mkdocs is set you can run:

mkdocs serve    # Change pages and see result in your local bowser

or

mkdocs build    # Create manual pages

cd $BDS_SRC
./git/commit    # Publish manual pages (if in master)

License

bds is open source.