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@martijnvermaat
martijnvermaat / playbook.yml
Last active Nov 22, 2016
Testcase for Ansible #18324
View playbook.yml
---
- hosts: all
tasks:
- include_vars: vars_plain.yml
- assert: that="var == 'vars_plain_yml'"
- include_vars: vars_vaulted.yml
- assert: that="var == 'vars_vaulted_yml'"
- include_vars: vars_plain
- assert: that="var == 'vars_plain'"
- include_vars: vars_vaulted
View keybase.md

Keybase proof

I hereby claim:

  • I am martijnvermaat on github.
  • I am martijnvermaat (https://keybase.io/martijnvermaat) on keybase.
  • I have a public key ASBU9sNz9RzOg8_nT4dssYbLszQejvkoSlY84KZDTpH_Dwo

To claim this, I am signing this object:

@martijnvermaat
martijnvermaat / auto-ssh-aliases.bash
Created May 11, 2016
Auto SSH session aliases for hosts configured in ~/.ssh/config
View auto-ssh-aliases.bash
# Auto SSH session aliases for hosts configured in ~/.ssh/config.
command_not_found_handle() {
if [[ ! "$1" ]] ; then
return 127
fi
if ! grep -q "^Host $1\$" ~/.ssh/config; then
return 127
fi
ssh $*
}
@martijnvermaat
martijnvermaat / nixos.md
Last active Nov 6, 2019
Installation of NixOS with encrypted root
View nixos.md
@martijnvermaat
martijnvermaat / README.md
Last active Apr 28, 2016
Genomic GenBank files and transcript identifiers
View README.md

Genomic GenBank files and transcript identifiers

Using the attached script we check all genomic GenBank files in the server cache for the transcript_id field in their mRNA features.

Using the cache from mutalyzer.nl

Category Files checked Transcripts With ID Without ID %
NG_ 3076 5989 5978 11 0.2 %
View manual.md

Quick introduction

Initial screen

When the program is started, the user is presented with a minimal pedigree consisting of a father, a mother and a child. On the left of the screen there is a slider for zooming in and zooming out.

In the top left corner three buttons can be seen, two of them (undo and redo) are greyed out. The third button is for downloading the pedigree.

In the top right corner two buttons can be seen, the left one (drawing view) is

@martijnvermaat
martijnvermaat / index.html
Created Feb 29, 2016
Merge rules with vendor-specific pseudo-element selectors
View index.html
<!doctype html>
<style>
#original input[type=range] {
-webkit-appearance: none !important;
}
#original input[type=range]::-webkit-slider-runnable-track {
height: 2px;
width: 100px;
background: red;
@martijnvermaat
martijnvermaat / server.py
Created Feb 5, 2016
SimpleHTTPServer with history API fallback
View server.py
#!/usr/bin/env python
"""
Modification of `python -m SimpleHTTPServer` with a fallback to /index.html
on requests for non-existing files.
This is useful when serving a static single page application using the HTML5
history API.
"""
@martijnvermaat
martijnvermaat / hgvs.md
Last active May 30, 2016
Operational semantics for HGVS
View hgvs.md

Operational semantics for HGVS

This formalisation is based on the idea that the meaning of a variant description is a set of fixed sequences projected on the referencesequence. (We call them replacements, but they can also be identities.) We explicitely do not mean the result (sequence) of applying these replacements. At least in my understanding, that is not how HGVS is intended to interpreted (and would also make it impossible to combine variants; how do you combine two plain sequences?).

@martijnvermaat
martijnvermaat / import.sh
Last active Mar 24, 2017
Mutalyzer transcript mapping imports
View import.sh
# NCBI36
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/MapView/Homo_sapiens/sequence/BUILD.36.3/initial_release/seq_gene.md.gz -O - \
| zcat | sort -t $'\t' -k 11,11 -k 2,2 > /tmp/hg18.seq_gene.sorted.md
mutalyzer-admin assemblies import-mapview -a hg18 /tmp/hg18.seq_gene.sorted.md 'reference'
mutalyzer-admin assemblies import-reference -a hg18 'NC_001807.4'
# GRCh37
wget ftp://ftp.ncbi.nlm.nih.gov/genomes/MapView/Homo_sapiens/sequence/ANNOTATION_RELEASE.105/initial_release/seq_gene.md.gz -O - \
| zcat | sort -t $'\t' -k 11,11 -k 2,2 > /tmp/hg19.seq_gene.sorted.md
mutalyzer-admin assemblies import-mapview -a hg19 /tmp/hg19.seq_gene.sorted.md 'GRCh37.p13-Primary Assembly'
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