John Lees' blog

Pathogens, informatics and modelling at EMBL-EBI

Display env variable, tmux and zsh over ssh

I have been using zsh within tmux, and found upon reattaching tmux X forwarding wasn’t working. For example when trying to launch gvim I’d get the error: E233: cannot open display The problem, a quick google determined, is that each time I ssh into my sever a new $DISPLAY environment variable is set. When I run ’tmux attach’ the new $DISPLAY variable is passed through (see http://stackoverflow.com/questions/8645053/how-do-i-start-tmux-with-my-current-environment) so any new windows within tmux will have the correct environment.

Compiling Stampy v1.0.23 for use with cortex - error: unrecognized command line option ‘-Wl’

To assemble illumina sequence data I am currently trialling assembly with cortex. To be able to use their Perl script to automate the pipeline between reads in and variant calls requires vcftools and stampy to be installed, and you provide the installation paths as input to the script. However when running make using the default downloaded stampy makefile I got the following error from g++ (v4.8.1): g++ \`python2.7-config --ldflags\` -pthread -shared -Wl build/linux-x86\_64-2.

Impute your whole genome from 23andme data

23andme is a service which types 602352 sites on your chromosomal DNA and your mtDNA. It is possible, by comparing to a reference panel in which all sites have been typed, to impute (fill in statistically) the missing sites and thus get an ’estimation’ of your whole genome. The piece of software impute2 written by B. N. Howie, P. Donnelly, and J. Marchini gives good accuracy when using the 1000 Genome Project as a reference.

A new direction for leesjohn

Since October 2013 I have stopped using Fedora, and instead use machines running Ubuntu 12.04/13.10, Windows 8 and OS X 10.8.5. As these OSs have a larger user base than Fedora, many of the issues I encounter are well documented and easy to fix (i.e. there is a stackexchange post as one of the top three google results), hence there haven’t been many things for me to post under the original remit of this blog.

A latex bibliography style I like (Nature style in biblatex)

This isn’t really a specific question, but I needed to make a bibliography in latex with the following requirements: The citations take up as little space as possible, so should probably be superscript The citations should be correctly grouped (i.e. 1-3, 6 not 6, 2, 3, 1) The bibliography can take up any amount of space The citations should be linked to their bibliography entry (i.e. hyperref compatible) bib entries contain unicode characters I want the entries to look like the Elsevier standard, though Nature is also fine I want DOIs, properly displayed and hyperlinked, not monospaced The style=nature option supplied to biblatex in the preamble (see http://ctan.