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Monthly Archives: May 2014

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. However the environment of any existing windows can’t be changed, causing the problem.

The best solution I found was proposed by Alex Teichman here: http://alexteichman.com/octo/blog/2014/01/01/x11-forwarding-and-terminal-multiplexers/
However I had two problems:

  1. It doesn’t seem to work with zsh rather than bash. I guess this is due to the behaviour of preexec() being different, but I couldn’t quickly work this out from the zsh manual.
  2. It maybe felt slightly inelegant to update $DISPLAY every single time a command is run

My solution is pretty similar. I add the following to ~/.zshrc:

echo $DISPLAY > ~/.display.txt
alias up_disp='export DISPLAY=`cat ~/.display.txt`'

This writes the correct $DISPLAY variable to a hidden file when a session is started (i.e. when I connect to the server). When I find forwarding isn’t working, I just run up_disp in that window.
Not the perfect solution, but it works ok for me

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_64-2.7-ucs4/pyx/maptools.o build/linux-x86_64-2.7-ucs4/c/map
utils.o build/linux-x86_64-2.7-ucs4/c/alignutils.o build/linux-x86_64-2.7-ucs4/readalign.o build/linux-x86_64-2.7-ucs4/algebras.o build/linux-x86_64-2.7-ucs4/frontend.o -o maptools.so
g++: error: unrecognized command line option ‘-Wl’

The solution was straightforward to find, as ever thanks to stackoverflow: http://stackoverflow.com/questions/21305309/g-doesnt-recognize-the-option-wl
All you need to do is edit lines 44 and 46 in the makefile, replacing the space after -Wl with a comma:

 43 ifeq ($(platform),linux-x86_64)
 44    g++ `$(python)-config --ldflags` -pthread -shared -Wl,$(objs) -o maptools.so
 45 else
 46    g++ `$(python)-config --ldflags` -pthread -dynamiclib -Wl,$(objs) -o maptools.so
 47 endif

As you can see from the surrounding if statement, this is only an issue on 64-bit linux platforms

I also tried compiling cortex with icc, but the compilation failed after a lot of errors. Rather than pursuing this further, I used gcc and only got warnings of unused variables in compilation