Notes about open source software, computers, other stuff.

Tag: Free Software (Page 2 of 2)

The Raspberry Pi runs ProbABEL

One of the first things I tried on my Raspberry Pi was to compile ProbABEL and see if it runs. Since the Raspberry Pi has an ARM processor I wasn’t sure whether our code was portable to it. Apparently it is! Compiling ProbABEL (r.1027 from SVN) took 30 minutes (single threaded of course) compared to 34 seconds on my Desktop (4 threads on an Intel Core i3 processor), but hey, it worked :-). Surprisingly it also passed all the checks in make check.

Once I hook up some more storage to device I will try to run ProbABEL on some real data. It will be interesting to see how much time it takes to run a linear regression on e.g. chromosome 22 of HapMap3 imputated data for a few hundred samples…

Will the Raspberry Pi be the next platform for GWAS ;-)?

ProbABEL 0.2.2 released

On November 7th I released version 0.2.2 of ProbABEL, a set of programs that allow scientists (usually geneticists and epidemiologists) to run Genome-wide association studies (GWAS) in a fast and efficient way, even on machines with low amounts of RAM.

ProbABEL is part of the GenABEL suite, wich is a set of open source package for statistical genomics. Its main developer is Yurii Aulchenko, my former supervisor at the Erasmus Medical Centre.

This update contains a few small bug fixes and an update of the probabel.pl wrapper script that enables the use of chunked imputation output files as input. For more detailed changes, check the announcement.
For those of you running Ubuntu Linux (or one of its derivatives and probably also Debian) I have set up the GenABEL PPA (personal package archive) where you can download and install the ProbABEL .deb package and stay up to date with future updates.
ProbABEL is also available for MS Windows, although we don’t have much experience running it on that platform.

Development of ProbABEL (and other members of the GenABEL suite) takes place on this R-forge page. If you are in search of an open source project to contribute to, feel free to contact us!

User support for the GenABEL suite can be found at our forum.

Testing for the presence of the “Eigen” headers using autoconf

For the ProbABEL project I’m working on I wanted to test for the presence of the Eigen header files using . Eigen is a C++ template library for linear algebra. It basically consists of a bunch of header files. On my PC the Eigen files are installed in /usr/include/eigen3/ since I used the Debian/Ubuntu libeigen3-dev package.

I first tried to test for the headers by simply including

AC_CHECK_HEADERS([eigen3/Eigen/Dense])

in configure.ac, but that didn’t work:

...
checking eigen3/Eigen/Dense usability... no
checking eigen3/Eigen/Dense presence... no
checking for eigen3/Eigen/Dense... no
...

It turns out that you have to add the following lines to configure.ac:

AC_LANG_PUSH([C++])
AC_CHECK_HEADERS([eigen3/Eigen/Dense])
AC_LANG_POP([C++])

Now I get the following output when running ./configure:

...
checking how to run the C++ preprocessor... g++ -E
checking eigen3/Eigen/Dense usability... yes
checking eigen3/Eigen/Dense presence... yes
checking for eigen3/Eigen/Dense... yes
...

To go into a bit more detail, these are the errors in config.log without the AC_LANG options:

...
configure:4877: checking eigen3/Eigen/Dense usability
configure:4877: gcc -c -g -O2 -Wall conftest.c >&5
In file included from /usr/include/eigen3/Eigen/Core:35:0,
                 from /usr/include/eigen3/Eigen/Dense:1,
                 from conftest.c:67:
/usr/include/eigen3/Eigen/src/Core/util/Macros.h:188:5: error: unknown type name 'namespace'
/usr/include/eigen3/Eigen/src/Core/util/Macros.h:188:21: error: expected '=', ',', ';', 'asm' or '__attribute__' before '{' token
In file included from /usr/include/eigen3/Eigen/Dense:1:0,
                 from conftest.c:67:
/usr/include/eigen3/Eigen/Core:98:12: error: expected identifier or '(' before string constant
In file included from /usr/include/eigen3/Eigen/Dense:1:0,
                 from conftest.c:67:
/usr/include/eigen3/Eigen/Core:144:18: fatal error: cerrno: No such file or directory
...

It seems to be the case that AC_LANG is set to C instead of C++ and consequently compilation of autoconf’s test programme fails. The AC_LANG_PUSH option forces autoconf to use C++.

Thanks to this post on Stack Overflow I could solve this problem.

Overwriting selected text in Emacs

I learned something new in Emacs (my favourite text editor) today. Normally in Emacs, if you start typing while having some text selected will not overwrite this text. This is contrary to what most people are used to in other editors. It turns out that Emacs has a minor mode that fixes this: delete-selection-mode. Add the following to your .emacs file to have it loaded by default:

(delete-selection-mode t)

Since delete-selection-mode enables transient-mark-mode I commented the line

(setq transient-mark-mode t)

in my .emacs

References:

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