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Installation

Containers

Here are the methods for installing with either Docker or Singularity.

docker pull staphb/lyveset:1.1.4f

singularity build lyveset.1.1.4f.sif docker://staphb/lyveset:1.1.4f

Requirements

  • Perl, multithreaded
    • BioPerl
  • BLAST+
  • Edirect (for downloading of test data)
  • GIT, SVN (for installation and updating)

Other requirements

Usually these packages are installed, but if you have a totally fresh system, you might want to consider installing the following

  • zlib
  • curses
  • zip/unzip
  • build-essential

Some Perl modules are needed in earlier versions of Lyve-SET including v1.1.4f.

  • File::Slurp
  • URI::Escape

Quickie Installation

  1. Run make install while you are in the Lyve-SET directory. This step probably takes 10-20 minutes.
  2. Update the path to include the scripts subdirectory. You can do this yourself if you are comfortable or run make env.
  3. Update your current session's path: source ~/.bashrc

In-depth Installation

Download the latest stable version from https://github.com/lskatz/lyve-SET/releases. You can also roll the dice by getting the cutting edge version with git.

tar -zxvf lyve-SET-1.1.4f.tar.gz
cd lyve-SET-1.1.4f.tar.gz
make install
make env

Other Installation Options

  • make install
  • make install-optional to install optional prerequisite software including bwa and snap
  • make env - update PATH and PERL5LIB in the ~/.bashrc file.
  • make check - check and see if you have all the prerequisites
  • make test - run a test phage dataset provided by CFSAN
  • make help - for other make options
  • make clean - clean up an old installation in preparation for a new installation

Fine details

  • make install-* - Many other installation options are available including but not limited to:
    • make install-smalt
    • make install-CGP
    • make install-samtools
  • make clean-* - Every make install command comes with a make clean command, e.g.:
    • make clean-CGP

Upgrading

By stable releases

Unfortunately the best way to get the next stable release is to download the full version like usual, followed by make install. If successful, then delete the directory containing the older version.

cd ~/tmp
wget https://github.com/lskatz/lyve-SET/archive/v1.1.4f.tar.gz
tar zxvf release.tar.gz
cd Lyve-SET
make install # takes 10-20 minutes to download packages on broadband; install
cd ~/bin
rm -r Lyve-SET && mv ~/tmp/Lyve-SET .

By git

git pull -u origin master
make clean
make install