Commit 9a97edb9 authored by Laros's avatar Laros

Merge branch 'patch-1' into 'master'

Patch 1

See merge request !10
parents c1ad5d36 c5ed8603
# Work discussion 11-04-2017
Present: Jonathan Vis (JV), Leon Mei (LM),
Mark Santcroos (MS), Pieter Neerincx (PN), Gerben van der Vries (GV),
Roan Kanninga (RK). Henk-Jan Zilverberg (HZ), Niels Idsinga (NI)
## GoNL re-analysis
- RK started a version describing exact commands used for GoNL pipeline. PH already provided his input.
- GoNL spec will be freezed by Thursday.
- RK asked about if we should use the new QUAL option in GATK (by default off in GATK 3.7 but on in GATK 4.0). Our current proposal is to use it and test it based on GIB's high confidence variant calls.
## eLAN
Resolved.
## CoManage
- HZ has LDAP server up running at Groningen site. They are waiting for the CoManage instance at SURF.
- MS commented that we can log in to CoManage now (PN should have details). But MS still has problems getting it running properly. MS suggested to contact Gerben (SURFSara) for support.
- Communication to Gerben (SURFSara) should be copied with both LUMC and Groningen teams. NI will try configuration tomorrow.
- We don't have problems with the SQL database used for CoManage at SURF anymore.
- PN wanted to have a test/acceptance instance of IDP at Groningen for testing.
## Ansible and Easybuild integration
- GV fixed the Molgenis-compute env. Currently deployed at the home dir of GV. GV will deploy the env at bbmri-nl share.
- PN is improving the ansible playbook (e.g., replacing wget in shell with native Ansible commands). Available at bbmri-nl github.
- PN had an Ansible issue. Login shells of Ansible are not interactive, so current work around is to sourcing (e.g., bashrc) explicitly in Ansible. MS will check PN's
work around solution to see if it is reasonable.
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