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View snakemake_3.9.0+dfsg-1_amd64.build
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 <kdmfoss@gmail.com>
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
View update-julia.sh
#!/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}
View tara
tara init af2573173e19a6ada1ab4a3486468336e05607e9
Wed Jun 8 15:26:44 2016 +1000
View mpmc_queue.hh
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)
{
View rundebcitest
#!/bin/bash
if [ $# -lt 1 ]
then
echo "USAGE: run-debci-test <PKG.changes> [<outdir>]"
exit 1
fi
if [ $# -eq 2 ]
then
View download-all-debmed-dupstreammeta.sh
for pkg in $(cat allpkgs)
do
mkdir -p "${pkg}"
wget -nv -O "${pkg}/upstream_metadata" \
"http://anonscm.debian.org/cgit/debian-med/${pkg}.git/plain/debian/upstream/metadata" \
|| rm -f "${pkg}/upstream_metadata"
done
View eigencalc.cc
/*
* ============================================================================
*
* Filename: eigencalc.cc
* License: GPLv3+
* Author: Kevin Murray, spam@kdmurray.id.au
*
* ============================================================================
*/
View tst.py
from __future__ import print_function, division
from frisk.kmerhash import *
import screed
from matplotlib import pyplot as plt
from functools import partial
import multiprocessing as mp
from os import path
def seq_ivom(gen):
View tst.py
from frisk.kmerhash import *
import screed
r = screed.open('/home/kevin/ws/seqs/TAIR10_gen/TAIR10.fasta.gz')
for x in r:
seq = x.sequence[:100000]
break
winsz = 3000
ivs = []
View code_challenge_5.py
# given a sequence find kmers of a given length that occur equal to t or more
# times in a given length of window in the sequence
from collections import deque
def kmer_frequency(text, k, window, thresh=3):
counts = dict()
kmers = deque()
for w in range(len(text)-window+1):
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