Beams-Galaxy wrapper local installation

beams_galaxy_wrapper-README.md

Create local BEAMS Conda package

> git clone https://github.com/computational-metabolomics/beams.git

Add metadata.yaml and build.sh files to the project - links meta.yaml and build.sh

> conda build beams

On mac you need to run this with write permissions

> sudo conda build beams

This will build the conda package and add it to your local conda build directory (we will need this CONDA_BLD_PATH full path later. On mac its usually /users/<username>/miniconda3/conda-bld)

Clone BEAMS-Galaxy wrapper tool and run galaxy using palanemo

Clone BEAMS-Galaxy wrapper tool from github

> git clone https://github.com/computational-metabolomics/beams-galaxy
> git checkout development # if branch doesnt exist ~ git fetch development
> cd <beams-galaxy_project_location>/tools/beams

If you don't have planemo setup

> virtualenv .venv; . .venv/bin/activate
> pip install "pip>=7" # Upgrade pip if needed.
> pip install planemo

Start galaxy server - Planemo (specify the galaxy server location and the conda channels for it to recognise the beams package)

> planemo serve --galaxy_root=<galaxy_server_location> --conda_exec=<conda_executable_location> --conda_channels=<conda_packages_location>,conda-forge

conda needs other dependencise so you have to add conda-forge to the conda-channels list