jfear

// Place your key bindings in this file to override the defaults
[
    // The following are Kevin's keybindings for VSCode
    // They are made available under CC BY 4.0
    //
    // To navigate
    // `==` denote sections
    // `---` denotes subsections
    //
    // == Dendron

jfear

#!/bin/bash

# I personally would merge sample across lane. Gzip file can just be concated
# together and as long as R1 and R2 are done in the same order it should work
# fine.
#
# going from
# - 1860_Time_0_S1_L001_R1_001.fastq.gz
# - 1860_Time_0_S1_L002_R1_001.fastq.gz
# - 1860_Time_0_S1_L002_R1_001.fastq.gz

jfear

#!/usr/bin/env python3
import logging
from logging.handlers import RotatingFileHandler
import sys

import colorama

def configure_logging():
    # enable cross-platform colored output
    colorama.init()

jfear

More recent resolution:

1. cd ~/../../etc (go to etc folder in WSL).
2. echo "[network]" | sudo tee wsl.conf (Create wsl.conf file and add the first line).
3. echo "generateResolvConf = false" | sudo tee -a wsl.conf (Append wsl.conf the next line).
4. wsl --terminate Debian (Terminate WSL in Windows cmd, in case is Ubuntu not Debian).
5. cd ~/../../etc (go to etc folder in WSL).
6. sudo rm -Rf resolv.conf (Delete the resolv.conf file).
7. In windows cmd, ps or terminal with the vpn connected do: Get-NetIPInterface or ipconfig /all for get the dns primary and
secondary.

jfear

def flatten_nested(content: Union[list, dict, ChainMap]) -> List[Union[str, int, float]]:
    """Flatten an arbitrary nested dictionary.

    Useful for flattening file patterns from a Yaml config.

    Example:
        >>> content = {"one": ["one_a", "one_b"], "two": "two_a"}
        >>> sorted(flatten_nested(content))
        ["one_a", "one_b", "two_a"]

jfear

#!/bin/bash -e

toolbox rm --force fedora-toolbox-32

echo "## Creating development container..."
toolbox create

run="toolbox run"

echo "## Updating Image"

jfear

Copyright (c) 2021 Justin M. Fear

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all

jfear

#!/bin/bash
conda create -n jupyter jupyterlab jupytext nodejs nb_conda ipywidgets nbdime ipympl jupyterlab-git
source activate jupyter
jupyter labextension install @jupyter-widgets/jupyterlab-manager
jupyter labextension install jupyterlab_vim
jupyter labextension install @jupyterlab/git
jupyter serverextension enable --py jupyterlab_git
jupyter labextension install @jupyterlab/toc
jupyter labextension install jupyterlab_bokeh
jupyter labextension install @ijmbarr/jupyterlab_spellchecker

jfear

README

Create a template service file at /etc/systemd/system/secure-tunnel@.service. The template parameter will correspond to the name of target host:

[Unit]
Description=Setup a secure tunnel to %I
After=network.target

jfear

"""Plot heatmap of all genes.

Plots the tpm normalized zscores of all genes as a heatmap.
"""
import numpy as np
import pandas as pd
from scipy.stats import fisher_exact
import matplotlib as mpl
from matplotlib.gridspec import GridSpec, GridSpecFromSubplotSpec
import matplotlib.pyplot as plt