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I hereby claim:

  • I am mikedacre on github.
  • I am mike_dacre (https://keybase.io/mike_dacre) on keybase.
  • I have a public key ASD_6hbCTlnvDAXei37EX6ct2rknqNWR-QKRzTSVhj7MNwo

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@MikeDacre
MikeDacre / RENEW.md
Last active April 3, 2022 21:11
These are the instructions I use myself for my annual GPG key renewal. I am sharing them here to help others, though they are not perfect.

Renewing the GPG Key

The point is to renew the core signing key, encryption key, and authentication key, and to create a set of subkeys to be used on devices without access to the GPG card.

The encryption key should not 'expire' ever, as it is needed for communication, the same is true for the parent key, which should never be anywhere other than the card and the veracrypt container. We give them an expiration date anyway, so that if something happens and I can't renew them, they eventually become invalud.

@MikeDacre
MikeDacre / cloudflare_refresh_nginx.sh
Created September 12, 2017 19:52
Sync cloudflare IPs with NGINX
# Based on https://support.cloudflare.com/hc/en-us/articles/200170706-How-do-I-restore-original-visitor-IP-with-Nginx-
# Save this file to /usr/bin/clodflare_refresh_nginx.sh
# Add the line "include /etc/nginx/global/cloudflare-ip.conf" to the server
# block of every nginx site you wish to expose the real IP for
# Add crontab (run a 03:05 every day): 5 3 * * * /usr/bin/clodflare_refresh_nginx.sh >/dev/null 2>&1
NGINX_CONF=/etc/nginx/global/cloudflare-ip.conf
curl https://www.cloudflare.com/ips-v4 | perl -p -e 's/^(.*)$/set_real_ip_from \1;/g' > $NGINX_CONF
curl https://www.cloudflare.com/ips-v6 | perl -p -e 's/^(.*)$/set_real_ip_from \1;/g' >> $NGINX_CONF
# use any of the following two
echo "real_ip_header CF-Connecting-IP;" >> $NGINX_CONF
@MikeDacre
MikeDacre / pascal.py
Created June 9, 2017 02:19
Run PASCAL: Allows easy running of https://www2.unil.ch/cbg/index.php?title=Pascal from any path
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Rewrite of the shell script for easy running from anywhere with cluster support.
Place this in the root of pascal and link to it from your path
"""
from __future__ import print_function
import os as _os
import sys as _sys
@MikeDacre
MikeDacre / Filter by multiple columns.ipynb
Last active May 25, 2017 16:34
Make a pandas DataFrame unique on multiple columns while preserving other columns and filtering
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@MikeDacre
MikeDacre / filter_dataframe.py
Last active May 25, 2017 16:35
A python 3 function to make a pandas DataFrame unique on multiple columns while preserving other columns and filtering by multiple columns
def run_filter(df, group_cols: list, merge_col: str, sort_col: str, cutoff: float = 0.6):
"""Make a DataFrame unique on group_cols based on boolean merge_col and float sort_col.
Picks most frequent result of boolean merge_col if the result represents a portion of the
total greater than cutoff. Then sorts the results ascending by sort_col and returns the
first row only.
If filter fails (i.e. top hit is less than cutoff of total) then the entire group is dropped.
Parameters
@MikeDacre
MikeDacre / Use SQLAlchemy with the UCSC Database.ipynb
Created February 9, 2017 19:17
Use SQLAlchemy with the UCSC Genome Database
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@MikeDacre
MikeDacre / troubleshoot.txt
Created November 18, 2016 02:50
jupyter troubleshoot outpyt
$PATH:
/usr/local/anaconda3/bin
/usr/local/anaconda3/bin
/home/dacre/bin
/usr/local/sbin
/usr/local/bin
/usr/bin
/home/dacre/usr/bin
/usr/local/MATLAB/R2013a/bin
/usr/lib/jvm/default/bin
+ [pyenv:24] enable -f /home/dacre/.pyenv/libexec/../libexec/pyenv-realpath.dylib realpath
+ [pyenv:30] '[' -z '' ']'
++ [pyenv:32] type -p greadlink readlink
++ [pyenv:32] head -1
+ [pyenv:32] READLINK=/usr/bin/readlink
+ [pyenv:33] '[' -n /usr/bin/readlink ']'
+ [pyenv:54] '[' -z /home/dacre/.pyenv ']'
+ [pyenv:57] PYENV_ROOT=/home/dacre/.pyenv
+ [pyenv:59] export PYENV_ROOT
+ [pyenv:62] '[' -z '' ']'
@MikeDacre
MikeDacre / .cvimrc
Last active September 22, 2016 20:51
My cVimrc
" Settings
" set nohud
" set nosmoothscroll
" set noautofocus " The opposite of autofocus; this setting stops
" sites from focusing on an input box when they load
set typelinkhints
let searchlimit = 30
let scrollstep = 70
let barposition = "bottom"