Commit 0ce00725 authored by Laros's avatar Laros

Merge branch 'master' of

parents a45c8d72 2a33ff15
# Work discussion 11-10-2016
Present: Leon Mei (LM), Jonathan Vis (JV), Jeroen Laros (JL).
## eLAN
- No update, we need an IP from Groningen to test.
## CoManage
- No update.
## Tool deployment
Hackathon was a success.
- Ansible Eazybuild role tested successfully.
- Peter is working on an Easybuild Ansible module (full integration with
- Combination Ansible / BioConda is working, demonstration on 14-10-2016.
- Ansible BioConda role is working.
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# Work discussion 25-10-2016
Present: Leon Mei (LM), Jonathan Vis (JV), Jeroen Laros (JL).
## eLAN
- Groningen will get an IP from the public space of SURF.
## CoManage
- Irene Nooren sent a proposal for a pilot with CoManage:
- Set up CoManage in the SURFsara cloud.
- Set up an LDAP domain.
- Connect the BBMRI VM(s) to this LDAP domain.
- Manage the domain with CoManage.
- Estimated time for implementation 3 man-month in total (1 for installation,
2 for testing and acceptance).
## Tool deployment
- Peter run into a permission error while executing an EazyBuild command,
probably this is a depenancy issue in the toolchain. Pieter and Gerben are
- Installing Galaxy via Ansible is successful, installing reference data
however, is removed from this playbook. There is a semi-manual workaround
available for now.
- LM had a meeting with Stefan Klein (Rotterdam, Imaging). The solutions
presented (Ansible, etc.) were received very well. Stefan is going to promote
automatic tool deployment solutions in other (imaging related) projects.
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# Work discussion 08-11-2016
Present: Jonathan Vis (JV), Jeroen Laros (JL).
## eLAN
- Groningen will get an IP from the public space of SURF.
## CoManage
No updates at this moment, Jeroen will visit SURF on the 14th of November.
## Tool deployment
- Leon is planning skype call (might be today at 3pm) with Pieter and Gerben to
continue on EasyBuild+Ansible integration.
- Leon discussed the pipeline progress tracking interface with Thomas Kroes
(WP3 pipeline developer working at LUMC-LKEB). His preliminary version was
demonstrated at the last BBMRI workshop. We confirmed that architecture is
generic enough so that we could use it to track our NGS pipeline structure
(as .dot file) and progress (exposed via a REST API by the pipeline execution
manager, e.g., biopet or Molgenis-compute). Perhaps a link to the APIs system
built by Jeroen/Jonathon now at the LUMC. Thomas will update our discussion
with WP3 developers and we will follow up a meeting in ~2-3 weeks to outline
- Leon got ansible script to install Galaxy working
( Installation of
reference datasets is now a separate step. But the Galaxy team is working on
a more integrated solution and hopefully it will help us to address this
problem soon.
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# Work discussion 06-12-2016
Present: Jonathan Vis (JV), Leon Mei (LM).
## eLAN
Paul van Dijk (SURF) is planning a meeting for the design of a structural
solution. The idea is to use one routing server per institute, but if this is
not possible for some reason, the institutes could peer BGP between each other.
This does not scale, but for now it might be a workaround.
## CoManage
PN mentions (via mail) that he will get a test environment for authorisation
workflows. The installation of CoManage can be done with an Ansible/Vagrant
combination, but setting up an identity provider is a lot more work. SURF is
going to assist in setting up such an environment.
## Tool deployment
- Annique Claringbould from Groningen likes to run the BIOS pipeline in Groningen.
They tested the Ansible role; some improvements should be made. This is ongoing.
- Proposed collaboration between wp 5 and wp 3 on the visualization of pipeline
progress. Monthly meetings are proposed; the first meeting is planned (January).
# Work discussion 31-01-2017
Present: Jonathan Vis (JV), Leon Mei (LM), Jeroen Laros (JL),
Pieter Neerincx (PN)
Starting Feb 1 Mark Santcroos will start in Leiden.
## eLAN
Operational between Surf, Leiden and Groningen (pinging works from Leiden to
Now a stress test should be conducted; random data (small and large files)
and/or data from the BIOS project.
## CoManage
CoManage is set-up at Surf and is ready for testing.
PN likes to use CoManage for account management on the newly ordered cluster in
PN wants to build an authorization workflow in CoManage.
## Re-run GONL
PN will recreate the workflow. Use GONL as a reference set for variant liftover
from build 37 to build 38.
## Ansible and Easybuild integration
LM proposes a hands-on session in February (week of the 20th).
Build the dependency graphs for molgenis compute and biopet.
March 16 meeting at Surf
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