View acct_parse.py
""" | |
Provides functions for the purpose of parsing a Sun Grid Engine (SGE) | |
accounting file for job metadata. | |
""" | |
__author__ = "Sam Nicholls <msn@aber.ac.uk>" | |
__copyright__ = "Copyright (c) Sam Nicholls" | |
__version__ = "0.0.32" | |
__maintainer__ = "Sam Nicholls <msn@aber.ac.uk>" |
View http-get-dos.conf
# Fail2Ban configuration file | |
# | |
# NOTE | |
# You should set up in the jail.conf file, the maxretry and findtime carefully in order to avoid false positives. | |
# | |
# Author: http://www.go2linux.org | |
# Modified by: samnicholls.net | |
# * Mon 6 Jun 2016 - Updated failregex to capture HOST group correctly | |
[Definition] |
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" |
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 |
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", |
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"]) |
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