This contains Bash scripts that deploy a SeqWare cluster with pan-cancer customizations for Bindle
Currently, this playbook has a dependency on seqware-bag which needs to be checked out in a directory with the same parent directory.
The sample_configs directory contains a number of config files in order to install a pan-cancer cluster either as a cluster or as a single note, with BWA installed or without.
The TCGA/ICGC PanCancer project is using Bindle to create analytical nodes/clusters for use with a BWA Workflow and downstream variant calling workflows. This project is using a variety of cloud technologies including VirtualBox, OpenStack, and vCloud. For each environment we use Bindle to create SeqWare environments that utilize Oozie-SGE. This allows researchers to write workflows using SeqWare but also analytical pipelines that simply use SGE and "qsub" to process data.
Here are some examples, you will want to customize the ~/.bindle/platform.cfg
to include the settings for the particular cloud environment you are working in (EBI, BioNimbus, DKFZ, Korea, etc). Each cloud will provide you the specifics such as account name, API keys, and which cloud technology to use.
# launch, use the correct command line args for you
perl bin/launch_cluster.pl --config=openstack --custom-params=<cluster-name>
Please see the PanCancer Wiki for more information about this project.
!!! Important !!! If running this on EBI or other cloud where large memory instances are not available, enable the "SGE hack" by passing sge_hack and swap_on as variables on the command line or throught the Bindle configuration file.