aaronwolen

# access aws credentials for a profile from ~/.aws/credentials
import boto3

profile = 'default'
session = boto3.Session(profile_name=profile)
credentials = session.get_credentials()
credentials.access_key
credentials.secret_key

aaronwolen

#!/usr/bin/env bash

# format
sudo mkfs -t ext4 /dev/nvme1n1

# mount ebs volumne
sudo mkdir -p /mnt/data
sudo mount /dev/nvme1n1 /mnt/data

# fix permissions

aaronwolen

while read line; do
  mv -v "$line" "${line// -  /}"
done < <(find . -name '* .png')

aaronwolen

# genome reference
fai_url := s3://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai
fai_file := $(notdir $(fai_url))

# original clinvar vcf
vcf_url := ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar_20210710.vcf.gz
raw_vcf := $(notdir $(vcf_url))

# modified vcf file
mod_vcf := $(raw_vcf:%.vcf.gz=%_modified.vcf.gz)

aaronwolen

library(osfr)
library(purrr)
library(tibble)


# functions ---------------------------------------------------------------

 # id: project GUID
.osf_list_wikis <- function(id) {
  api_path <- sprintf("nodes/%s/wikis", id)

aaronwolen

# Code written by brentp in response to BioStars question:
# http://www.biostars.org/post/show/6544/

import random
import sys

def write_random_records(fqa, fqb, N=100000):
    """ get N random headers from a fastq file without reading the
    whole thing into memory"""
    records = sum(1 for _ in open(fqa)) / 4

aaronwolen

 ##############################################################################
 #                        Calendar Heatmap                                    #
 #                                by                                          #
 #                         Paul Bleicher                                      #
 # an R version of a graphic from:                                            #
 # http://stat-computing.org/dataexpo/2009/posters/wicklin-allison.pdf        #
 #  requires lattice, chron, grid packages                                    #
 ############################################################################## 

## calendarHeat: An R function to display time-series data as a calendar heatmap 

aaronwolen

#!/usr/bin/env bash

# variables
#############
tilevcf="dist/bin/tiledbvcf"
tmpdir="/mnt/data/tmp"
samplefile="$tmpdir/samples.txt"

output_dir="data"
export_dir="$output_dir/exports"

aaronwolen

- alias: Announce Door Open
  trigger:
    - platform: state
      entity_id:
        - binary_sensor.back_door
        - binary_sensor.front_door
      to: 'on'
      for: 
        seconds: 30

aaronwolen