willfurnass

function tau_a = shear_stress(D, Q, k_s, T, den)
    %{ Hydraulic shear stress at pipe wall (in Pa).
    %
    % Params:
    % D -- internal diameter (m)
    % Q -- flow (m^3s^-1)
    % k_s -- roughness height (m)
    % T -- temperature; defaults to 10degC)
    % den -- density defaults to 1000kg/m^3
    % 

willfurnass

--- BibTeX.js.orig	2015-07-03 07:18:37.000000000 +0100
+++ BibTeX.js	2015-08-09 14:21:08.779706944 +0100
@@ -1176,7 +1176,11 @@
 		if(!type) type = "misc";
 		
 		// create a unique citation key
-		var citekey = buildCiteKey(item, citekeys);
+		if (item.shortTitle==''){
+		    var citekey = buildCiteKey(item, citekeys);
+		} else {

willfurnass

import numpy as np

myriad_codes = np.array((
    None, None, None, None, "HP", None, None,
    None, None, None, "HT", "HU", None, None,
    None, "HW", "HX", "HY", "HZ", None, None,
    "NA", "NB", "NC", "ND", None, None, None,
    "NF", "NG", "NH", "NJ", "NK", None, None,
    "NL", "NM", "NN", "NO", None, None, None,
    None, "NR", "NS", "NT", "NU", None, None,

willfurnass

#!/usr/bin/env python

# A test of whether Ruffus can be used to submit jobs to a cluster using the
# DRMAA API, sharing the DRMAA session between threads to allow multiple jobs to
# be submitted at once without burdening the head node with multiple DRMAA
# sessions.

# Can run this from a conda environnment created using
# conda create -n drmaatest -c bioconda python=2.7 ruffus drmaa

willfurnass

#!/usr/bin/env python
from __future__ import print_function
from ruffus import transform, suffix, pipeline_run

# A test of using Ruffus to locally run a very simple pipeline comprised of
# tasks defined as Python functions

# Can run this from a conda environnment created using
# conda create -n drmaatest -c bioconda python=2.7 ruffus drmaa

willfurnass

#!/bin/sh
# David Jones and Will Furnass (University of Sheffield)

# `qrsh` is often the most convenient utility for starting interactive shell
# sessions on Sun/Son of Grid Engine (SGE) clusters but it has some limitations (as
# configured on the ShARC/Iceberg clusters):
# 
# - none of the standard SGE environment vars (e.g. JOB_ID, PE_HOSTFILE,
#   NSLOTS) that are defined in qsub/qsh batch/interactive sessions are set
#   (annoying but not the end of the world);

willfurnass

tmux tips

Default prefix: <ctrl>b

Session management

• tmux new -s session_name - creates a new tmux session named session_name
• tmux a - attach to first available session
• tmux attach -t session_name - attaches to an existing tmux session named session_name
• tmux switch -t session_name - switches to an existing session named session_name

willfurnass

Random Grid Engine tips and tricks

The following work with Son of Grid Engine (SGE) 8.1.9 as configured on the University of Sheffield's ShARC and Iceberg clusters.

Jobs with dependancies

You can use the -hold_jid <<job-name or job-name>> option to make jobs run only when other jobs have finished, rather than having jobs start and sit waiting for other tasks to complete.

willfurnass

Initialise a git repository:

cd somedir
git init

Install git subrepo if you haven't done so already:

https://github.com/ingydotnet/git-subrepo#installation

willfurnass

#!/bin/bash
# Will Furnass
# Oct 2017

if [[ $# -lt 1 ]]; then
    echo 1>&2 "Extract list of user email addresses from Synology DSS '.dss' config dump"
    exit 1
fi

dss_path="$1"