biobakery_wiki - biobakery/biobakery GitHub Wiki
bioBakery
Quick Start: Local Compute
Vagrantbox
- Install Virtualbox and Vagrant
- Download and unpack bioBakery
- Run bioBakery by double clicking (or executing from the command line) the file for your operating system
- Linux and MacOS:
start_biobakery.command
- Windows:
start_biobakery.bat
Please note the first time you run bioBakery it will download and extract the box (~10 GB in size). This can take a bit of time depending on your internet connection. When you run bioBakery in the future, it will start up much faster (~30 seconds).
Conda
After installing
Conda,
set up your channels so the biobakery repository is at the top of your
list. Next run the command $ conda install $TOOL -c biobakery
,
replacing $TOOL
with the name of the tool. For a short tutorial on how
to install and run a demo using a bioBakery Conda package, see the
section on bioBakery Conda
packages.
Docker
After installing Docker, run the
command $ docker pull biobakery/$TOOL
, replacing $TOOL
with the name
of the tool. For a short tutorial on how to install and run a demo in a
biobakery Docker container, see the section on bioBakery Docker
images.
Quick Start: Cloud Compute
Google Cloud
The biobakery tool suite is available pre-installed on a Google Cloud
image (Ubuntu 18.04) from the bucket:
biobakery_bucket/biobakery_image_v1.7.tar.gz
. For more information see
the section on bioBakery in Google
Cloud.
Amazon Web Services
The biobakery tool suite is also available pre-installed on an AMI (Ubuntu 16.04 plus miniconda) from Amazon Market Place, search for "biobakery" from the "Community AMIs" list. For more information see the section on bioBakery in Amazon EC2 .
Please note, due to conflicting dependencies the bioBakery tools
installed on the cloud images (GCE and AMI) and the Vagrantbox are each
installed in their own conda environment. To obtain a list of all of the
conda environments on each image run $ conda env list
.
Please see the sections and links that follow for detailed information about bioBakery.
Overview
bioBakery is an easy to use, virtual environment that provides a platform for the research community to use the Huttenhower tools without having to install the tool suite directly on their personal machines. This documentation provides in depth instructions on all topics related to bioBakery (installation, basic setup and advanced configuration).
We provide support for bioBakery users. Please join the bioBakery users google group and feel free to post questions directly to the group or by emailing [email protected].
Please select one of the three options for documentation.
- Basic usage provides information about installation, basic setup, how to run a demo, and sharing documents and folders
- Advanced configuration documents useful tools for advanced users on how to run bioBakery with modified components of the virtual environment
- Internal documentation is for the Huttenhower Lab users and other members of the bioinformatics community to document the mechanism of bioBakery (e.g. how to add new tools and package and release new virtual images etc.)
We strongly recommend new users read the Basic Usage documentation to get started.