View add_user_accounts.sh
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#!/usr/bin/env bash | |
##### | |
# Set default command line options | |
##### | |
USERNAME_PREFIX=user | |
USERNAME_SUFFIX_START=1 | |
USERNAME_SUFFIX_END=100 | |
USERNAME_SUFFIX_ZERO_PADDING_LENGTH=4 |
View trackList.json
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"fmtDetailValue_Dbxref" : "function(dbxref){if(typeof dbxref!='string'){return dbxref}var dbid=dbxref.split(':');var prefix='';switch(dbid[0].toLowerCase()){case 'interpro':prefix='http://www.ebi.ac.uk/interpro/entry/';break;case 'pfam':prefix='http://pfam.sanger.ac.uk/family/';break;case 'reactome':prefix='http://www.reactome.org/content/detail/';break;case 'unipathway':prefix='http://www.grenoble.prabi.fr/obiwarehouse/unipathway/upa?upid=';break;case 'kegg':prefix='http://www.genome.jp/kegg-bin/show_pathway?ec';break;case 'prositepatterns':prefix='http://prosite.expasy.org/';break;case 'prositeprofiles':prefix='http://prosite.expasy.org/cgi-bin/prosite/PSView.cgi?ac=';break;case 'smart':prefix='http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN=';break;case 'superfamily':prefix='http://supfam.org/SUPERFAMILY/cgi-bin/scop.cgi?sunid=';dbid[1]=dbid[1].replace('SSF','');break;case 'gene3d':prefix='http://www.cathdb.info/version/latest/superfamily/';dbid[1]=dbid[2];break;case 'pirsf':prefi |
View gff3_split.pl
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#!/usr/bin/env perl | |
use strict; | |
use warnings; | |
my $bed_file = shift @ARGV; | |
my $suffix_fmt = '_part%01d'; | |
open(my $bed_fh, '<', $bed_file) || die "Couldn't open BED file: $!\n"; | |
my %cut_positions; |
View depth2bedgraph.awk
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#!/usr/bin/awk | |
# Takes output of "samtools depth" and reformats into grouped bedgraph format: | |
# samtools depth -r ${loc} -Q 1 --reference $fasta $bam | mawk -f scripts/depth2bedgraph.awk > /tmp/my.bedgraph | |
# Example input: | |
#chr1 26 2 | |
#chr1 27 2 | |
#chr1 28 2 | |
#chr1 29 5 | |
#chr1 30 5 | |
#chr1 31 5 |
View mlFASTA2slFASTA.sh
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#!/bin/bash | |
# Convert a multi-line FASTA file into a single line FASTA file | |
# These are easier/faster to process using native UNIX tools like paste - - < in.fasta | |
dos2unix | awk 'BEGIN { RS = "\n>"; FS = "\n"; OFS = "" }; | |
{ | |
if (NR == 1) { | |
print $1 | |
} else | |
if (NR > 1) { | |
print ">"$1 |
View update_openstack_python_apis.sh
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#!/bin/bash | |
sudo apt-get update && sudo apt-get -y dist-upgrade | |
urls=( | |
'https://github.com/pypa/pip.git' | |
'git://github.com/openstack-dev/pbr.git' | |
'git://github.com/iguananaut/d2to1.git' | |
'https://github.com/kelp404/six.git' | |
'https://github.com/openstack/python-glanceclient.git' | |
'https://github.com/openstack/python-keystoneclient.git' |
View sra_process.sh
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#!/bin/bash | |
# Bash script to download a bunch of *.sra files from the NCBI SRA, using | |
# the aspera client, and extract FASTQ data using the SRA Toolkit. | |
max_bandwidth_mbps=50 | |
# These SRA files are for the durum genome | |
files=( | |
'SRR567512.sra' | |
'SRR567559.sra' |
View install.sh
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#!/bin/bash | |
# You should clone this gist to obtain the installation and patch file | |
# and then run it locally, after changing the below settings to something | |
# suitable for your system. Something like this: | |
# sudo apt-get install -y ssh | |
# cd | |
# scp -r nhaigh@bioserver:git/sysadmin/generic/gitorious_install ./ | |
# Edit the settings below, then run the following as root: | |
# cd gitorious_install && sh ./install.sh | |
# |
View gist:5589673
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#!/bin/bash | |
# First setup everything needed for connecting to it via an NX connection | |
wget https://gist.github.com/nathanhaigh/4007406/raw/40717e3031bec9efccc3dfcc38c3a50c222d29d9/NXServer.sh | |
chmod +x NXServer.sh | |
./NXServer.sh | |
apt-get -y install libreoffice-java-common htop sysstat git xclip dos2unix | |
wget http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz | |
tar xzf install-tl-unx.tar.gz && rm install-tl-unx.tar.gz |
View screenrc
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# Get/install this screenrc file using something like this (the URL is specific to a particular revision, update as needed): | |
# wget https://gist.github.com/nathanhaigh/5200267/raw/17c8e4a95df8540dfb5a8374c8f78c1f2568e43f/screenrc -O ~/.screenrc | |
startup_message off | |
caption string "%?%F%{= Bk}%? %C%A %D %d-%m-%Y %{= kB} %t%= %?%F%{= Bk}%:%{= wk}%? %n " | |
hardstatus alwayslastline | |
hardstatus string '%{= kG}[ %{G}%H %{g}][%= %{= kw}%?%-Lw%?%{r}(%{W}%n*%f%t%?(%u)%?%{r})%{w}%?%+Lw%?%?%= %{g}][%{R} %d/%m %{W}%c %{g}]' | |
altscreen on |
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