Workshop SIG - Compute Resources for Life Science Research (CRLS)
Date: 15 MAR 2017
In the Special Interest Group (SIG) Compute Resources for Life Science Research (CRLS) we shared lessons learned and best practices, and discussed requirements, used cases and models to scale out or federate compute resources and data processing workflows.
- 15 Mar 2017
- SURF, Utrecht
- Prior knowledge needed?
- Meeting type
Topic: Reproducible pipelines – integration with software stack
During this SIG CRLS meeting we discussed the integration and synchronisation of software stacks with automatic pipeline deployment. Several speakers presented solutions that are being used in their departments, including solutions for HPC environments, and shared their experience.
|09.00 - 09.30 hrs||Registration & Coffee|
|09.30 - 09.45 hrs||Welcome and introduction, Irene Nooren (SURFsara) & Patrick Kemmeren (Princes Maxima Centrum)|
|09.45 - 10.15 hrs||NFU Data4Lifesciences WP7 status update, Irene Nooren|
|10.15 - 11.00 hrs||Autodeployment of reproducible BBMRI-NL WGS and RNAseq analysis pipelines with Ansible, BioConda and EasyBuild, Leon Mei (LUMC)|
|11.00 - 11.15 hrs||Coffee break|
|11.15 - 12.00 hrs||Deploying software with GNU Guix on a multi-user HPC environment, Roel Janssen (UMCU)|
|12.00 - 12.45 hrs||Jupyter notebooks, Machiel Jansen (SURFsara)|
|12.45 - 13.00 hrs||Wrap up, Irene Nooren & Patrick Kemmeren|
|13.00 - 14.00 hrs||Lunch|
- Status update NFU Data4lifesciences WP7 by Irene Nooren
- Autodeployment of reproducible pipelines by Leon Mei
- GNU Guix for maintaining a HPC software stack by Roel Janssen
- Jupyter notebooks by Machiel Jansen
This workshop was intended for researchers, research supporters and ICT-managers.