kdm9

mmseqs2 = function (seqs, db, threads=24, preamble="mamba activate mmseqs2;") {
    id = uuid::UUIDgenerate()
    tmpdir = glue::glue("tmp/{id}")
    dir.create(tmpdir, recursive = T)
    fafile = glue::glue("{tmpdir}/input.fa")
    writeLines(paste(sprintf(">%d", seq_along(seqs)), seqs, sep = "\n"), fafile)
    
    cmd = glue::glue(
        "{preamble} ",

kdm9

kview = function(df) {
    fn = paste0(tempfile(), ".tsv")
    readr::write_tsv(df, fn, na="")
    system(sprintf("libreoffice --calc %s", fn))
    return(invisible(df))
}

kdm9

#!/bin/bash
set -xe
mkdir -p ~/.local/opt
cd ~/.local/opt
wget -O git-annex-standalone-amd64.tar.gz https://downloads.kitenet.net/git-annex/linux/current/git-annex-standalone-amd64.tar.gz
rm -rf git-annex.linux
tar xvf  git-annex-standalone-amd64.tar.gz
mkdir -p ~/.local/bin
ln -sf $PWD/git-annex.linux/{git,git-annex,git-annex-shell,git-receive-pack,git-upload-pack,git-shell} ~/.local/bin
set +x

kdm9

as.numeric.verbose = function(x) {
    # this code will parse german-style comma-as-decimal numbers or
    # english-style dot-as-decimal numbers.
    x = ifelse(grepl('^\\d+,\\d+$', x, perl=T), sub(',', '.', x, fixed=T), x)
    x.num = as.numeric(x)
    # Find which values got coerced to NA
    coerced = which(!is.na(x) & is.na(x.num))
    if (length(coerced) > 0) {
        cat("Following values coerced to NA:\n")
        print(paste(coerced, x[coerced]))

kdm9

#!/bin/bash

echo "This is the Chromosome 4 finder script"

grep '^Chr2' data/genes.bed > data/chr4.bed
wc -l data/chr4.bed

kdm9

dpkg-checkbuilddeps: error: Unmet build dependencies: python3-pytools
W: Unmet build-dependency in source
dpkg-buildpackage: info: source package snakemake
dpkg-buildpackage: info: source version 3.9.0+dfsg-1
dpkg-buildpackage: info: source distribution UNRELEASED
dpkg-buildpackage: info: source changed by Kevin Murray <[email protected]>
 dpkg-source --before-build snakemake
dpkg-source: info: applying 0001-Use-the-inbuild-sphinx.ext.napoleon.patch
dpkg-source: info: applying 0003-Use-debian-s-mathjax-package.patch
dpkg-source: info: applying 0003-Compat-fix.patch

kdm9

#!/bin/bash

declare -A urls
urls[0.5]='https://s3.amazonaws.com/julialang/bin/linux/x64/0.5/julia-0.5-latest-linux-x86_64.tar.gz'
urls[nightly]='https://s3.amazonaws.com/julianightlies/bin/linux/x64/julia-latest-linux64.tar.gz'

set -xeuo pipefail
MAINVER=0.5
PREFIX=${PREFIX:-$HOME}

kdm9

tara init af2573173e19a6ada1ab4a3486468336e05607e9
Wed Jun 8 15:26:44 2016 +1000

kdm9

template<typename Data>
class concurrent_queue
{
private:
    std::queue<Data> the_queue;
    mutable std::mutex the_mutex;
    std::condition_variable the_condition_variable;
public:
    void push(Data const& data)
    {

kdm9

#!/bin/bash

if [ $# -lt 1 ]
then
	echo "USAGE: run-debci-test <PKG.changes> [<outdir>]"
	exit 1
fi

if [ $# -eq 2 ]
then