biocyberman

[2013-08-18 09:34]  INFO  11:34:24,077 HelpFormatter - --------------------------------------------------------------------------------
[2013-08-18 09:34]  INFO  11:34:24,077 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.6-5-gba531bd, Compiled 2013/07/18 18:05:31
[2013-08-18 09:34]  INFO  11:34:24,078 HelpFormatter - Copyright (c) 2010 The Broad Institute
[2013-08-18 09:34]  INFO  11:34:24,078 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
[2013-08-18 09:34]  INFO  11:34:24,081 HelpFormatter - Program Args: -T CallableLoci -R /usr/local/share/bcbio-nextgen/genomes/Hsapiens/hg19/seq/hg19.fa -I /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2.bam --out /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-split/tx/tmpn8kdHQ/WES01_WES01_SQ1_FT2-chr19-callable.bed --summary /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-callable-summary.txt -L /data/proj01/work/prealign/WESF120601_B1_FT2/WES01_WES01_SQ1_FT2-calla

biocyberman

1	14425	15103
1	15669	15990
1	16589	17074
1	17176	18448
1	19008	19209
1	20561	20763
1	24446	24915
1	29226	29428
1	30273	30513

biocyberman

#!/bin/bash

# Build latest version of Emacs, version management with stow
# OS: Tested on Ubuntu 12.04 LTS onward 
# version: 25.1
# Toolkit: lucid

set -e

readonly version="26.2"

biocyberman

running ediff over byobu ssh sessions has poor colors. I can't see color markings, therefore it's difficult to do diff and merge.

For emacs itself

https://gist.github.com/choppsv1/e8198df70cb1778b04d6 (Managed to improved color without this patch)

remove ubuntu tmux
tmux upgrade from github https://github.com/tmux/tmux. Also need to compile and install http://libevent.org/ for tmux

For bybou

biocyberman

#!/usr/bin/env Rscript
args = commandArgs(trailingOnly=TRUE)
                                        # test if there is at least one argument: if not, return an error
if (length(args)==0) {
  stop("Please provide prefix for output", call.=FALSE)
} else if (length(args)==1) {
  ## default bin size
  args[2] = 500
}

biocyberman

import std.stdio;
import std.conv : to;
import std.datetime.stopwatch: benchmark, Duration;

mixin template kroundup32(T) {
  // string mstr = "String from template";
  void kroundup32(ref T x){
    // pragma(inline, true);
    --x;
    x|=x>>1;

biocyberman

#!/usr/bin/env Rscript
## Date: Tue Aug 7 10:43:27 2018
## Last modified Time-stamp: <2018-08-10 12:54:38 CEST (vql)>
## Author: Vang Quy Le
## Organization: Aalborg University Hospital

## Copyright 2018 Vang Quy Le
##
##  This file is free software: you may copy, redistribute and/or modify it
##  under the terms of the GNU General Public License as published by the

biocyberman

"""
Compare mutations from augur vs direct naive calcuation 
"""

import sys
from Bio import Phylo, SeqIO
import numpy as np

from augur.translate import construct_mut
from augur.utils import read_node_data

biocyberman

#!/bin/bash
#####################################################
# Name: Bash CheatSheet for Mac OSX
# 
# A little overlook of the Bash basics
#
# Usage:
#
# Author: J. Le Coupanec
# Date: 2014/11/04

biocyberman

# Content of ~/.byobu/.tmux.conf
# Set zsh as default shell for AD users who can't change default shell easily
set -g default-shell /usr/bin/zsh
set -g default-command /usr/bin/zsh
# Extend display time for panes number. This allows using `F12 q <pane_number>` to jump to the pane/split quickly. 
set -g display-panes-time 2500