andreas-wilm

#!/bin/bash

#SBATCH --job-name=bwaindex
#SBATCH --output=bwaindex.out
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --time=01:00:00
#SBATCH --mem-per-cpu=20000

SIF=/shared/containers/dnazoo-uwa-20191106.sif

andreas-wilm

import urllib.parse

TEMPLATEURL = "https://portal.azure.com/#create/Microsoft.Template/uri/"

def toraw(ghurl):
    # convert github url to its raw equivalent, if needed
    ghbase = "https://github.com"
    ghrawbase = "https://raw.githubusercontent.com"
    if ghbase in ghurl and "/blob/" in ghurl:
        return ghurl.replace(ghbase, ghrawbase).replace("/blob/", "/")

andreas-wilm

// modify the following two values as needed
DECLARE @dataVersion string = "mag-YYYY-MM-DD";
DECLARE @blobAccount string = "XXX";

DECLARE @uriPrefix   string = "wasb://" + @dataVersion + "@" + @blobAccount + "/";
DECLARE @outFile string = "/Output/patent_languages.tsv";

@Papers = Papers(@uriPrefix);
@PaperLanguages = PaperLanguages(@uriPrefix);

andreas-wilm

#!/usr/bin/env python

import sys
import json

DEF_PRIO = 'M'
added_task = json.loads(sys.stdin.readline())
if 'priority' not in added_task:
    sys.stderr.write("Adding default priority: {}\n".format(DEF_PRIO))
    added_task['priority'] = DEF_PRIO

andreas-wilm

DECLARE @dataVersion string = "mag-2019-03-22";
DECLARE @blobAccount string = "<PLACEHOLDER>";
DECLARE @uriPrefix   string = "wasb://" + @dataVersion + "@" + @blobAccount + "/";
DECLARE @typeCounts string = "/Output/TypeCounts.tsv";

@Papers = Papers(@uriPrefix);

@Types = SELECT
    DocType, COUNT(1) AS cnt
FROM

andreas-wilm

#!/bin/env python


import csv
import sys

import numpy


trace = sys.argv[1]

andreas-wilm

# https://www.sylabs.io/guides/3.0/user-guide/quick_start.html#quick-installation-steps

# https://unix.stackexchange.com/questions/1338/what-is-the-fedora-equivalent-of-the-debian-build-essential-package
sudo yum install make automake gcc gcc-c++ kernel-devel
sudo yum install openssl-devel libuuid-devel

# install go
export VERSION=1.11 OS=linux ARCH=amd64
cd /tmp
wget https://dl.google.com/go/go$VERSION.$OS-$ARCH.tar.gz

andreas-wilm

# https://docs.aws.amazon.com/AWSEC2/latest/UserGuide/raid-config.html
nvmes=$(sudo lsblk | awk '/^nvme/ {printf "/dev/%s ", $1}')
sudo mdadm --create --verbose /dev/md0 --level=0 --name=my_raid --raid-devices=$(echo $nvmes | wc -w) $nvmes
sleep 10# crutch
sudo mkfs.ext4 -L my_raid /dev/md0
sudo mdadm --detail --scan | sudo tee -a /etc/mdadm.conf
sudo dracut -H -f /boot/initramfs-$(uname -r).img $(uname -r)
sudo mkdir /data
sudo mount LABEL=my_raid /data
sudo chown ec2-user:ec2-user /data/

andreas-wilm

#!/bin/bash

csv=$1
test -z "$csv" && exit 1
test -e "$csv" || exit 1
grep -q '^AccessKeyId' $csv || exit 1
test $(cat "$csv" | wc -l) -eq 2 || exit 1

akid=$(tail -n1 $csv  | cut -d',' -f 2)
sak=$(tail -n1 $csv  | cut -d',' -f 2)

andreas-wilm

import hts

var b: BGZ
open(b, "example.txt.gz", mode="rb")
set_threads(b, 2)

var kstr: kstring_t
kstr.l = 0
kstr.m = 0
kstr.s = nil