MikeDacre

[opts]

[queue]
max_jobs = 1000
sleep_len = 2
queue_update = 5

[prof_default]
cores = 1
mem = 4000

MikeDacre

#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""Submit a bunch of jobs."""
import sys
import argparse
from time import sleep
import cluster


CMD = '/home/dacre/mike_tools/bin/rename_mesh_snps.py {bed} -i {infile} -o {outfile}'

MikeDacre

" 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"

MikeDacre

+ [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

$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

MikeDacre

MikeDacre

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

#!/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

# 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