Commit b58a3ea4 authored by Laros's avatar Laros


parent 693afb97
# Work discussion 25-04-2017
Present: Jonathan Vis (JV), Mark Santcroos (MS), Pieter Neerincx (PN),
Gerben van der Vries (GV), Peter van 't Hof (PH).
## GoNL re-analysis
- Scratch space on Shark nodes: /tmp (approx. 1TB) no auto delete;
- Roan is not here today, so details remain unclear: PN asks Roan to schedule an
extra meeting with PH;
- No full pipeline run on Shark yet;
- PH asks about LTS.
## eLAN
## CoManage
- 11 May hands-on day @ Surf Amsterdam;
- Only LDAP (vs LDAPS) problem in Groningen;
- MS: first focus on POC for the workflow, later worry about protocols;
- Upgrade CoManage.
## Ansible and Easybuild integration
- GV: Tools installed on Shark. Reference files: /exports/genomes (PH).
- GV: Test jobs submitted.
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# Work discussion 25-04-2017
Present: Jonathan Vis (JV), Pieter Neerincx (PN), Gerben van der Vries (GV),
Peter van 't Hof (PH), Jeroen Laros (JL), Rowan Kanninga (RK), Leon Mei (LM).
## GoNL re-analysis
- GV: Started testing with the Molgenis framework, Experienced some memory
issues. They seem to be solved now.
- Some tools in the pipeline were updated (R + R scripts), input for cutadapt
(reverse complement) was fixed.
- Check cutadapt sequences, BWA and R version, AP: LM.
- Picard module 2.9.0 on UMCG cluster is pointing to the wrong version. AP: PN.
- Reinstall of pipelines via EasyBuild before running the pipeline.
- Estimated time: 4 days for 32 samples (10 trios, + 2 twins).
- PN: We need to check concordance, array and liftover before we deliver.
- PH asks about LTS, AP JL and LM.
## eLAN
## CoManage
- PN: Has worked on authorisation workflow. Potential issues with multiple
group memberships and deleting on of these groups. Do we do this locally or
globally? Meeting at SURF, this Thursday.
- LM: Do we need other people (DICT, Leiden).
- Gained some enthusiasm from the admins in Groningen.
- No test-IDP at the UMCG.
## Ansible and Easybuild integration
- PN made an idempotent playbook, checking handlers now.
## Closing remarks
- LM will contact the Imaging WP about Ansible.
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