Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
bbmri2
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
Issues
0
Issues
0
List
Boards
Labels
Service Desk
Milestones
Merge Requests
0
Merge Requests
0
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Incidents
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Wiki
Wiki
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Create a new issue
Jobs
Commits
Issue Boards
Open sidebar
Laros
bbmri2
Commits
f87814e1
Commit
f87814e1
authored
Mar 28, 2017
by
Laros
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Update notes_2017_03_28.md
parent
c8ee4dde
Changes
2
Hide whitespace changes
Inline
Side-by-side
Showing
2 changed files
with
39 additions
and
41 deletions
+39
-41
notes/wd/notes_2017_02_28.md
notes/wd/notes_2017_02_28.md
+0
-41
notes/wd/notes_2017_03_28.md
notes/wd/notes_2017_03_28.md
+39
-0
No files found.
notes/wd/notes_2017_02_28.md
deleted
100644 → 0
View file @
c8ee4dde
# Work discussion 14-02-2017
Present: Jonathan Vis (JV), Leon Mei (LM), Jeroen Laros (JL),
Pieter Neerincx (PN), Peter van 't Hof (PH), Gerben van der Vries (GV).
## GoNL re-analysis
Sample naming convention:
-
We use the exising GoNL IDs that have no connection to biobanks.
-
PhiX in the reference sequence. This was also asked in a VKGL meeting, there
was a preference to include it.
-
Phase by transmission still needed, the haplotype caller does not take trio
date into account.
-
Trio aware variant calling on one trio to compare to the haplotype caller.
Ansible installation testing is still needed. Especially the EasyBuild part is
challenging. PN and GV are going to do this.
10T reserved at the LUMC for this analysis.
## eLAN
Stress test still needed.
-
Part of the GoNL project.
## CoManage
Authorisation workflow:
-
Creating a VO succeeded.
-
A lot of options, no good overview.
-
PN suggests a hackathon (Gerben Venekamp, PN, Mark Santcroos) PN will
schedule this.
-
Local enrollment, we first let UMCG and LUMC come up with solutions which we
will use as a template for other UMCs.
## Ansible and Easybuild integration
Usable at this moment.
-
Nothing discussed about packaging.
-
Ansible role working, needs to be documented.
-
Ansible plugin is in the POC phase.
\ No newline at end of file
notes/wd/notes_2017_03_28.md
0 → 100644
View file @
f87814e1
# Work discussion 14-02-2017
Present: Jonathan Vis (JV), Leon Mei (LM), Jeroen Laros (JL),
Mark Santcroos (MS), Pieter Neerincx (PN), Gerben van der Vries (GV),
Roan Kanninga (RK).
## GoNL re-analysis
Refset proposal:
-
PN and JL are going to send this to the NCBI.
-
The VKGL will be contacted for feedback.
RK: We should enable base recalibration.
-
Can we use multiple recalibration files on the fly?
-
If so, compare to the 'polished BAM' method.
QC:
-
BAM statistics.
-
Concordance with both array data and hg19-VCFs.
## eLAN
Test succeeded.
## CoManage
PN, MS, GV, Paul van Dijk had a hands-on session.
-
Problems with the SQL database.
-
An other meeting in April for an authorisation workflow.
-
Before this, we need a test LDAP server in Groningen.
-
MS has an LDAP server running, waiting for a firewall setting.
Rens (SURF) wants to test CoManage on the (new) BIOS VM.
## Ansible and Easybuild integration
Ansible installation testing:
-
GV succeeded installing easybuild via ansible on Shark.
\ No newline at end of file
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment