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Overview

Bayesian phylogentic programs like MrBayes and BEAST work better when the BEAGLE library is installed. BEAGLE provides these programs with an MCMC sampler using CPU-based or GPU-based computation. Therefore, before compiling or using MrBayes and BEAST, BEAGLE and other prerequisites must be set-up and installed first. Unfortunately, setting-up all these software and libraries can become pretty frustrating very quickly.

Here I show how to properly set-up these programs to keep your frustration to a minimum. Broadly speaking, these instructions are applicable for Windows, Mac, and Linux. However, because I am specifically recounting my own experiencing setting-up my Linux machine, the more detailed parts of this guide focuses on installing on Linux.

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# Run this script in the directory where you want to save the conda-lock file at
# Activate env to make a `conda-lock.yml` file of
# conda activate venv
# Export env spec list using conda/mamba as `environment.yml`
conda env export > environment.yml
# Make conda-lock file
# Edit platform tag `-p` 
# For multiple platforms just add more, e.g. `-p osx-64 -p linux-64`
conda-lock -f environment.yml -p linux-64
# When new packages are installed, the conda environment changes and 

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# FIRST, Activate env to add to Jupyter, e.g. venv
# conda activate venv
# Then run this script
# Edit ENV_NAME variable to name the kernel
# Kernel names can only contain ASCII letters and numbers and these separators: - . _ (hyphen, period, and underscore).
# This will be the label in JupyterLab
ENV_NAME=Conda
# Install ipykernel via conda/mamba
conda install ipykernel
# Add current active environment

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How to mount a VirtualBox shared folder when the Guest OS boots

Problem

While using VirtualBox's Guest Additions to mount shared folders provides a seamless way to mount shared folders, there are also disadvantages.

• Shared folders will always mount in /media/sf_(share name) unless specified using through vbox drivers in the guest OS
• Mounting does not happen at boot-time. Applications that require paths at boot will not be able to access the shared folder even after it is mounted - such as Docker.

Solution

Instead of relying on Guest Additions, if you have sudo permissions, shared folders can be mounted at boot-time using fstab. Using this approach allows

kentwait

version: '3.3'
services:
    lab:
        ports:
            - '10000:8888'
        container_name: datascience-notebook
        volumes:
            - '${PWD}:/home/jovyan/work'
        image: jupyter/datascience-notebook
        

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# On remote (c24.local)
jupyter notebook --no-browser --port=10000

# On current computer
# create a tunnel that runs in the bg
# first set of name:port is local, second set is remote
ssh -f -N -L localhost:10024:localhost:10000 kent@c24.local

kentwait

three_to_one_aa = {
  'Ala': 'A',
  'Arg': 'R',
  'Asn': 'N',
  'Asp': 'D',
  'Asx': 'B',
  'Cys': 'C',
  'Glu': 'E',
  'Gln': 'Q',
  'Glx': 'Z',

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[Down]  o:50403.85      h:50444.31      l:50222.59      c:50303.48      hao:50410.95    hac:50343.5575  vol:4420.06
[Down]  o:50302.05      h:50313.53      l:50120.15      c:50226.84      hao:50352.95    hac:50240.6425  vol:5617.008
[Down]  o:50226.84      h:50309.2       l:50151 c:50209.99      hao:50264.445   hac:50224.25749999999   vol:3995.061
[Up]    o:50210 h:50393.25      l:50150 c:50160.01      hao:50218.42    hac:50228.315   vol:6494.194
[Down]  o:50160 h:50173.02      l:49730 c:49769.26      hao:50185       hac:49958.07    vol:26268.227
[Down]  o:49769.26      h:49950 l:49612.18      c:49772.69      hao:49964.630000000005  hac:49776.0325  vol:13958.26
[Down]  o:49772.69      h:49789.86      l:49314.14      c:49571.64      hao:49770.975000000006  hac:49612.082500000004  vol:18062.925
[Down]  o:49571.64      h:49680 l:49477.44      c:49660.64      hao:49672.165   hac:49597.43000000001   vol:6384.345
[Up]    o:49660.64      h:49787 l:49410 c:49756.91      hao:49616.14    hac:49653.637500000004  vol:887

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[Up]    HeikinAshiKlineSummary { open_time: 1629733620000, open: 49660.65, high: 49679.19, low: 49623.77, close: 49653.49, volume: 340.212, close_time: 1629733679999, quote_asset_volume: 16891095.04434, number_of_trades: 3343, taker_buy_base_asset_volume: 126.96, taker_buy_quote_asset_volume: 6303688.27145, ha_open: 49647.985, ha_high: inf, ha_low: 49623.77, ha_close: 49654.274999999994 }
[Down]  HeikinAshiKlineSummary { open_time: 1629733680000, open: 49653.49, high: 49677.32, low: 49635.24, close: 49660.0, volume: 212.477, close_time: 1629733739999, quote_asset_volume: 10551853.58003, number_of_trades: 2612, taker_buy_base_asset_volume: 117.889, taker_buy_quote_asset_volume: 5854917.85542, ha_open: 49657.07, ha_high: inf, ha_low: 49635.24, ha_close: 49656.5125 }
[Down]  HeikinAshiKlineSummary { open_time: 1629733740000, open: 49659.82, high: 49674.26, low: 49629.0, close: 49630.01, volume: 169.779, close_time: 1629733799999, quote_asset_volume: 8428987.70956, number_of_trades: 2096, taker_buy_base_asset_vol

kentwait

HOWTO init a ReactJS-Tauri app in Mac OS

The following instructions have worked for me running Mac OS 11.4.0 X64 with Node.js 16.4.0, Rust 1.53 and Tauri 1.0.0-beta.4.

Init a ReactJS app using npm

First, cd to parent directory where the root directory of the app will be located, ie: /home/me/src. Use the following command to generate the react directory structure: