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Sam Nicholls SamStudio8

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SamStudio8 / go.sh
Created Jun 16, 2020
building the kraken2-microbial database
View go.sh
# kraken2-microbial database
## Monday 3rd September 2018
## s.nicholls.1
KDB=$1
kraken2-build --download-taxonomy --threads 24 --db $KDB
kraken2-build --download-library archaea --db $KDB
kraken2-build --download-library bacteria --db $KDB
View override_docker_workflow.sh
#!/bin/bash
USER_ID=${LOCAL_USER_ID:-9001}
echo "starting with UID : $USER_ID"
echo "creating RAMPART user"
useradd --shell /bin/bash -u $USER_ID -o -c "" -m rampart
echo "raising RAMPART on $CLIENT $SERVER"
@SamStudio8
SamStudio8 / list_counties.sh
Last active Mar 23, 2020
Generate a list of UK authorities
View list_counties.sh
rm counties.*
rm *csv
# England ######################################################################
curl -O -J -L https://www.registers.service.gov.uk/registers/local-authority-eng/download-csv
# https://www.datadictionary.nhs.uk/data_dictionary/nhs_business_definitions/l/local_authority_de.asp?
# A Local Authority, in relation to England is:
## a County Council
awk -F',' '$6=="CTY" {print $7}' local-authority-eng.csv >> counties.eng.ls
@SamStudio8
SamStudio8 / shredder.py
Last active Mar 11, 2020
A very bad read generator
View shredder.py
import argparse
import sys
View contiguity.R
library(tidyverse)
assemblies=read_tsv('kraken_summary.bond.tsv')
short_name <- c(
"Bacillus subtilis" = "bs",
"Cryptococcus neoformans" = "cn",
"Enterococcus faecalis" = "ef",
"Escherichia coli" = "ec",
"Lactobacillus fermentum" = "lf",
@SamStudio8
SamStudio8 / base.Dockerfile
Last active Aug 2, 2019
Compile gpu-racon for the ONT Promethion with CUDA 9.0.176
View base.Dockerfile
# grab an off the shelf container with cuda9
FROM nvidia/cuda:9.0-devel-ubuntu16.04
# update gcc to gcc-6 as the default gcc-5 is too old
RUN apt-get update && apt-get install -y software-properties-common wget git
RUN add-apt-repository ppa:ubuntu-toolchain-r/test
RUN apt-get update && apt-get install -y gcc-6 g++-6
# update cmake as the default is too old
RUN wget -qO- "https://cmake.org/files/v3.15/cmake-3.15.1-Linux-x86_64.tar.gz" | tar --strip-components=1 -xz -C /usr/
View get_pion_signal.sh
# A little bash script to download our juicy ONT PION data
# If this doesn't work for you, express your disappointment to @samstudio8.
# Use "EVEN" or "LOG" for $1, eg: `bash get_pion_signal.sh EVEN`
MODE=$1
echo "Fetching signal blocks. Don't be afraid to CRTL+C and resume if needed..."
for i in {00..25}
do
echo $i;
wget -c https://nanopore.s3.climb.ac.uk/Zymo-PromethION-$MODE-BB-SN_signal.tar.$i;
View kraken-lonelykmers.py
import sys
THRESHOLD = 0.25 # reads must have 25% of their k-mers assigned
for line in sys.stdin:
fields = line.strip().split()
kmers_fields = fields[4:]
total_kmers = sum([int(x.split(":")[1]) for x in kmers_fields])
unassigned_kmers = sum([int(x.split(":")[1]) for x in kmers_fields if x[0] == "0"])
View krakkening.sh
PATH=$PATH:/home/ubuntu/ware/blast/ncbi-blast-2.7.1+/bin;
kraken2-build --download-taxonomy --threads 24 --db /working/databases/kraken2-test/
kraken2-build --download-library archaea --db /working/databases/kraken2-test/
kraken2-build --download-library bacteria --db /working/databases/kraken2-test/
kraken2-build --download-library fungi --db /working/databases/kraken2-test/
kraken2-build --download-library protozoa --db /working/databases/kraken2-test/
kraken2-build --download-library viral --db /working/databases/kraken2-test/
kraken2-build --download-library UniVec_Core --db /working/databases/kraken2-test/
kraken2-build --threads 24 --build --db /working/databases/kraken2-test/
@SamStudio8
SamStudio8 / hearty.py
Created Jun 24, 2018
python-fitbit intraday heart
View hearty.py
import fitbit
import gather_keys_oauth2 as Oauth2
import datetime
CLIENT_ID = 'YOUR CLIENT'
CLIENT_SECRET = 'YOUR SECRET'
server = Oauth2.OAuth2Server(CLIENT_ID, CLIENT_SECRET)
server.browser_authorize()
ACCESS_TOKEN = str(server.fitbit.client.session.token['access_token'])
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