grep biotech | more
A blog about my experiences with bioinformatics, operating systems, and random other technologies and bits.
Wednesday, March 28, 2012
Monday, August 23, 2010
Monday, April 12, 2010
pfexec cp /usr/local/share/terminfo/x/xterm-256color /usr/share/lib/terminfo/x/
If you don't have this installed, and I'm not sure how I installed it, you can probably find it on a linux installation. Now back to work, in color!
Sunday, September 27, 2009
As the post seems to indicate, building gcc with --disable-concept-checks should fix the problem. This is the case for libSBML. It seems that disabled concept checks may be the default for gcc; I am not sure why my gcc build had them enabled originally (I suppose it is a good idea if you only have to worry about your own code).
Tuesday, July 21, 2009
which makes use of Solaris' FMA service (Fault Management):
Really, it would be nice to have email notifications set up and easily configurable. I didn't want to mess with syslog-ng, as I wasn't sure where to start (I certainly didn't want everything it finds emailed to me).
As always, you'll want to test that your mail gets past SPAM filters - you can do this with mailx from the command line. I edited the script to use mailx -r my_reply_address to keep it consistent with my testing (since gmail initially did mark my tests as spam). I also tested the script in VirtualBox to verify that it works when a hard drive that is part of a zpool goes missing.
Saturday, December 20, 2008
This is a rough build (no packages) of Blender 2.4.8a. Furthermore, it may only run on Intel Core2Duo systems, since I used -march=core2 and -mtune=core2 when building with gcc. This build was done without OpenAL; if you need this, let me know. All "make install"s for dependencies install in /usr/local, with the exception of blender itself, which does not appear to have a make install; instead, copy the directory to the desired location and create a script like the following to run Blender (say, at /usr/local/blender):
You will also need to have libstdc++.so (64bit) on your system; see the post below on building gcc if you need this. If you use this or have any suggestions, please let me know.
Friday, September 5, 2008
Wednesday, July 23, 2008
sage: a = int('1')
sage: b = Integer('1')
sage: a == b
sage: type(a) == type(b)
I love Sage, so maybe I'll come back to this later when I have more time. Right now, I think that if type(a) is contained in type(b) *and* a == b, then type(a) == type(b) should return true. But this brings up interesting questions about what are types ... I'll edit this entry more later once I've read up on more type theory, more category theory, and sage/python type handling design (this could be a while!).
Saturday, August 4, 2007
I've been doing a fair amount of coding lately, I don't feel like going in to details just yet. One project is CthughaNix, the resurrection of a great music visualization tool. Speaking of bring back things from the past, I started reading The Wheel of Time saga again, since there's only the last book left to be written. This was most likely a bad decision on my part as it is hard for me to put a book down and I'm fairly busy right now. The other project is work related – it is intended to be parametric alignment software eventually, but right now I'm finalizing regular global alignment and integrating it with EMBOSS.
Here's a SS of Cthughanix running in Solaris, but screen shots don't really do it justice:
Tuesday, July 3, 2007
At any rate, if you also have these problems (unlikely, but I know some of you are out there), here are the options I used to build GMP 4.2.1 with GCC 4.2.0 (prerelease):
CFLAGS and CXXFLAGS: -O3 -m32 -mcpu=7450 -mpowerpc -maltivec
make distclean && ./configure --enable-cxx ABI=32 && make && make check