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# 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 |
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#!/bin/bash | |
##################################################### | |
# Name: Bash CheatSheet for Mac OSX | |
# | |
# A little overlook of the Bash basics | |
# | |
# Usage: | |
# | |
# Author: J. Le Coupanec | |
# Date: 2014/11/04 |
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""" | |
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 |
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#!/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 |
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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; |
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#!/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 | |
} |
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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 |
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#!/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" |
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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 | |
1 35053 35491 |
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[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 |