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Jonathan Chang jonchang

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@jonchang
jonchang / mnt-net-cifs-example.automount
Created January 18, 2024 00:41
automount-example
[Unit]
Description=example cifs share automount
[Automount]
Where=/mnt/net/cifs/example
[Install]
WantedBy=multi-user.target
@jonchang
jonchang / test.py
Created March 8, 2022 23:11
concurrent.futures example
# concurrent.futures example
# - submits work to task pool asynchronously
# - post-process results as they come in
from concurrent.futures import ProcessPoolExecutor, as_completed
from time import sleep
from random import randint
def do_some_work(item):
@jonchang
jonchang / logs.md
Created April 22, 2020 12:28
icu4c 66.1 logs
test --verbose alexjs 
==> brew test --verbose alexjs
Testing alexjs
/usr/bin/sandbox-exec -f /private/tmp/homebrew20200421-31578-r3thdm.sb ruby -W0 -I $LOAD_PATH -- /usr/local/Homebrew/Library/Homebrew/test.rb /usr/local/Homebrew/Library/Taps/homebrew/homebrew-core/Formula/alexjs.rb --verbose
==> /usr/local/Cellar/alexjs/8.1.1/bin/alex test.txt 2>&1
sh: line 1: 31587 Abort trap: 6 /usr/local/Cellar/alexjs/8.1.1/bin/alex test.txt 2>&1
dyld: Library not loaded: /usr/local/opt/icu4c/lib/libicui18n.64.dylib
@jonchang
jonchang / unbottled.csv
Created February 5, 2020 07:03
number formula count percent
19 libtasn1 153,485 0.83
198 cocoapods 18,533 0.10
228 emacs 14,126 0.08
239 gdal 12,346 0.07
243 mono 11,922 0.06
331 libiconv 6,618 0.04
341 qemu 6,235 0.03
355 kafka 5,809 0.03
365 glfw 5,611 0.03
@jonchang
jonchang / fsc26.md
Last active January 6, 2020 20:23
applying the stick of correction to fastsimcoal

R error for P2C2M SNAPP:

dyld: Library not loaded: /usr/local/lib/libgomp.1.dylib
  Referenced from: /Users/jonchang/Downloads/Tutorial/example_mode1/./fsc26
  Reason: image not found

fsc26 is looking for GCC in the wrong place

Run mdfind to figure out where GCC actually is. It can't find libgomp.1.dylib so search for:

@jonchang
jonchang / brewver.R
Created September 10, 2019 08:29
#!/usr/bin/env Rscript
library(tidyverse)
req <- jsonlite::fromJSON("https://formulae.brew.sh/api/analytics/install-on-request/30d.json")$items
inst <- jsonlite::fromJSON("https://formulae.brew.sh/api/analytics/install/30d.json")$items
req <- req %>% transmute(formula, install_on_request = as.numeric(str_replace_all(count, ",", "")))
inst <- inst %>% transmute(formula, installs = as.numeric(str_replace_all(count, ",", "")))
@jonchang
jonchang / example.tex
Created February 24, 2018 22:45
Example LaTeX source for mcexam package
\documentclass[twoside]{article}
\usepackage[english]{babel}
% set fonts
\usepackage[utf8]{inputenc}
\usepackage[T1]{fontenc}
\usepackage{mathpazo}
\usepackage{microtype}
\usepackage{etoolbox}
@jonchang
jonchang / unconcatenate_phylip.py
Last active November 18, 2017 22:19
Unconcatenates a RAxML-style phylip/partitions file
#!/usr/bin/env python3
# By Jonathan Chang - September 2017
import sys, argparse, logging, re, os
def get_partitions(path):
"""Given a path, returns a dictionary with partition names as keys and a list of
length 2, representing a range of characters."""
@jonchang
jonchang / streaming_select_cols.py
Created December 10, 2014 00:07
select only certain columns from a tab delimited file (optionally gzipped)
#!/usr/bin/env python
from __future__ import print_function
import gzip
import argparse
from operator import itemgetter
def get_args():
parser = argparse.ArgumentParser(description="selects fields from a tab-delimited file")
@jonchang
jonchang / instructions.md
Last active August 29, 2015 14:05
building revbayes w/ homebrew boost

install homebrew... http://brew.sh

install dependencies

brew install cmake boost

pull down revbayes development version