grep biotech | more

ksh93 for bioinformatics

2010-08-23T21:49:00.001-05:00

From #illumos on Freenode:
alanc: I suspect anyone using ksh93 for bioinformatics is likely to be the thing under study
lol
* gdamore looks at roland.
yep, richlowe was right.

My favorite $TERM

2010-04-12T19:46:00.002-05:00

The default in opensolaris, xterm, was not nice. I copied a file:

pfexec cp /usr/local/share/terminfo/x/xterm-256color /usr/share/lib/terminfo/x/

then add:
export TERM=xterm-256color
to ~/.bashrc

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!

2009-09-27T13:34:00.008-05:00

If you are trying to build libSBML, you may run into a problem similar to this.
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).

Monitor hardware faults in Solaris

2009-07-21T17:45:00.005-05:00

I found the following script:
http://prefetch.net/code/fmadmnotifier

which makes use of Solaris' FMA service (Fault Management):
http://opensolaris.org/os/community/fm/

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.

Blender for Solaris X64 (Core2Duo)

2008-12-20T03:37:00.005-05:00

Download: Blender Bundle

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):

#!/bin/sh
LD_LIBRARY_PATH=/usr/gnu/lib/amd64:/usr/local/lib/amd64 /usr/local/blender-2.48a/obj/solaris-2.11-x86_64/bin/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.

Remove advertisement text from searched content

2008-09-05T22:29:00.002-05:00

Web search engines, google's included, need to remove (by default anyway) any text that appears to be coming from an advertisement in the page from the searched text of the page. I could talk more about why, but I think this is obvious.

Equality of elements should imply equality of types

2008-07-23T20:56:00.003-05:00

Unfortunately, few things are perfect. I'll leave it to someone else to tell me I'm wrong (or right?) here, but the following seems less than ideal:

sage: a = int('1')
sage: b = Integer('1')
sage: a == b
True
sage: type(a) == type(b)
False

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!).

Update 08/03/07

2007-08-04T00:34:00.001-05:00

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:

@import url("/v-css/278764212-blogger_main.css");
@import url("/v-css/1877526874-flexible_buttons.css");
@import url("/v-css/898437004-buttons.css");

@media tty {
i{content:"\";/*" "*/}} @import url("/v-css/1784484781-blogger_ie5win.css"); /*";}
}/* */

--> </style> <script src="https://ssl.google-analytics.com/urchin.js" type="text/javascript"> </script> <script type="text/javascript"> </script> <link href="css/blogger.css" type="text/css" rel="stylesheet"> <link href="css/buttons.css" type="text/css" rel="stylesheet"> <script type="text/javascript"> </script> <script src="/js/cookies.common.js" type="text/javascript"></script> <style type="text/css"> </style> <script src="app/scripts/dom.common.js" type="text/javascript"></script> <script src="app/scripts/post.images.js?ver=5" type="text/javascript"></script> <script type="text/javascript"> </script> <script type="text/javascript"> </script> </head> <body class="status-uploading"> <div id="body"><div id="main"><div id="m2"><div id="m3"> <div id="uploading"> <form onsubmit="return false;" name="uploader" id="uploader" action="/upload-image.do" method="post" enctype="multipart/form-data"> <input type="hidden" name="blogID" value="6320964608623059176"> <div id="image-locations"> <div id="add-from-disk" class="add"> <h2>Add <b>an image from your computer</b></h2> <div class="errorbox-good"> <input type="hidden" name="securityToken" value="QtpxqxxM3lOjdqs06oZ1j_92Kj4=:1186205661120"> </div> <p> <strong onclick="Images.addImageFileField();">Add another image</strong> <input unselectable="on" type="file" name="image-file0"> <span class="note">We accept jpg, gif, bmp and png images, 8 MB maximum size</span> </p> </div> <div id="add-from-web" class="add"> <h2>Or add <b>an image from the web</b></h2> <p> <strong onclick="Images.addImageWebField();">Add another image</strong> <span><b>URL</b><input type="text" name="image-web0"></span> </p> <p class="learn-more"> <a href="http://help.blogger.com/bin/answer.py?answer=42492" target="_blank">Learn more</a> about using web images </p> </div> </div> <div id="image-layout"> <div style="clear:both;"></div> <h2> Choose a layout. </h2> <div id="image-layout-positions" onselectstart="return false;"> <ul> <label for="layout-none"> <li class="none"> <input type="radio" id="layout-none" value="NONE" name="postImagesPosition"> None </li> </label> <label for="layout-left"> <li class="left"> <input type="radio" checked id="layout-left" value="LEFT" name="postImagesPosition"> Left </li> </label> <label for="layout-center"> <li class="center"> <input type="radio" id="layout-center" value="CENTER" name="postImagesPosition"> Center </li> </label> <label for="layout-right"> <li class="right"> <input type="radio" id="layout-right" value="RIGHT" name="postImagesPosition"> Right </li> </label> </ul> </div> <div id="image-layout-sizes"> <strong>Image size:</strong> <ul> <li class="right"> <input type="radio" id="layout-small" value="SMALL" name="postImagesSize"> <label for="layout-small">Small</label> </li> <li class="center"> <input type="radio" checked id="layout-medium" value="MEDIUM" name="postImagesSize"> <label for="layout-medium">Medium</label> </li> <li class="left"> <input type="radio" id="layout-large" value="LARGE" name="postImagesSize"> <label for="layout-large">Large</label> </li> </ul> <div id="image-layout-remember"> <input type="checkbox" checked name="keepThisLayout" value="true"> Use this layout every time? </div> </div> <div style="clear:both;"></div> </div> <div id="clickTrappingDiv"></div> <div id="button-wrap"> <div style="clear:both;"></div> <div id="postButtons"> <div class="ubtn-small"> <div class="ubtn-blue-on-white"> <script type="text/javascript">document.write(" \u003cdiv id\u003d\"cancel\" onclick\u003d\"if (this.className.indexOf("ubtn-disabled") \u003d\u003d -1) {window.close(); return false;}\" class\u003d\"ubtn\"\> \u003cdiv class\u003d\"i\"\> \u003cdiv class\u003d\"t\"\>\u003cdiv\> \u003c/div\>\u003c/div\> \u003ca href\u003d\"javascript:void(0)\" onclick\u003d\"return false;\" tabindex\u003d\"0\"\>\u003cspan\>Cancel\u003c/span\>\u003c/a\> \u003cdiv class\u003d\"b\"\>\u003cdiv\> \u003c/div\>\u003c/div\> \u003c/div\> \u003c/div\> ");</script> </div> </div> <div class="ubtn-small"> <div class="ubtn-orange-on-white"> <script type="text/javascript">document.write(" \u003cdiv id\u003d\"uploadButton\" onclick\u003d\"if (this.className.indexOf("ubtn-disabled") \u003d\u003d -1) {go(); return false;}\" class\u003d\"ubtn\"\> \u003cdiv class\u003d\"i\"\> \u003cdiv class\u003d\"t\"\>\u003cdiv\> \u003c/div\>\u003c/div\> \u003ca href\u003d\"javascript:void(0)\" onclick\u003d\"return false;\" tabindex\u003d\"2\"\>\u003cspan\>Upload Image\u003c/span\>\u003c/a\> \u003cdiv class\u003d\"b\"\>\u003cdiv\> \u003c/div\>\u003c/div\> \u003c/div\> \u003c/div\> ");</script> </div> </div> </div> </div> <div class="errorbox-bad"> <input type="checkbox" name="acceptTerms" value="true" onclick="toggleDisplay(d("clickTrappingDiv"))"> I accept the <a href="http://picasa.google.com/intl/en_US/web/tos.html" target="_blank">Terms of Service</a> <span id="tosUpdated">(Updated 12/13/06)</span> <div class="errormsg">You must accept the Terms of Service to upload photos.</div> </div> </form> </div> <div id="progress"> <div id="loading-message"> <h1>Loading</h1> <h2>Your images are being uploaded to Blogger.</h2> </div> <img src="img/icon_inprogress.gif' name='graphics1' height='421' border='0'/>

GMP 4.2.1 on OS X 10.3.9

2007-07-03T13:12:00.000-05:00

You don't want the same company that makes the iPhone to make your enterprise servers. Regardless, it seems I'm stuck with using a small OS X 10.3.9 cluster. We can't upgrade easily (I won't get in to the reasons, though some of them are partly Apple's fault of course), but suffice to say that despite having such a nice machine, we are stuck in the 32 bit land of the not so ancient OS X 10.3 and can't even get things like Java JDK 1.5 or 1.6 (an added incentive to upgrade to OS X 10.4 from Apple...).

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

Sun Consumer Products

2007-07-02T16:37:00.001-05:00

Open Solaris isn't perfect for the end user yet, but it has a lot of potential. I'd like to show my support to Sun by buying something from them. There's the media kit, but even though I'm just wanting to show my support I think media kits are kind of useless since Open Solaris is updated so frequently. Star Office appears to be free with Open Solaris, so no need to buy that either. The one thing I found that appeared to be useful and affordable was a plugin for Open Office or Star Office that gives you bogging functionality within the office application. This isn't much, but it is only $10.00 and it is something I can use regularly.

What I'd really like to see is an Open Solaris User membership. Members could vote for new value added features and get some minimal amount of tech support. The tech support is secondary to me however, voting is what Open Solaris needs. I don't know of any commercially driven OS that has such a support option (then again, I'm not keen on every Linux or BSD distribution and I don't get paid to blog). I got the idea from Transgaming's Cedega. Transgaming holds a monthly poll for its subscribers, and subscribers get to cast as many votes as they have subscriptions. To me this seems like a great way to run a software business, and it would be great if someone employed the model for an operating system. I hope that someone will be Sun, though admittedly my hopes aren't high.

The "simple" way to do things.

2007-06-30T13:43:00.001-05:00

Who wants to make play lists or keep an alarm clock when you have your laptop with you 23/24 hours each day?

Say I want to find all the songs with bach or mozart in the title and loop through them. This (somewhat long) one-liner will do the trick:

echo `find ./ -name '*[B|b]ach*' -o -name '*[M|m]ozart*' | xargs -I song echo "'song'"` | xargs mplayer -loop 0

(substitute mplayer with your favorite command line music player) There is probably a shorter way of accomplishing the same thing. If you find such a way, please post it!

Setting an alarm is much simpler. If you want to get up in 8 hours,

bash-3.00$ bc
8*3600
28800
quit
bash-3.00$ sleep 28800 && mplayer Shared/George\ Michael\ wham\ -\ wake_me_up_before_you_go_go.mp4

If you have a more regular sleep schedule (but then, why would you be reading this?) you may find setting up a cron job to play a song more useful.

Useful Solaris tips for Linux Users

2007-06-19T12:52:00.000-05:00

Since I'm coming from Linux, I thought it would be useful to start a long entry about Solaris tips for Linux users. I'll update this entry with new tips as I find them.

ldconfig and ld.so.conf solaris equivalents (taken from the blog of Chris Miles):

If you're a Linux admin on Solaris and are looking for the Solaris equivalent of ldconfig and /etc/ld.so.conf read on.

The command you are looking for is crle(1) - this is the equivalent of Linux's ldconfig but even more powerful. Read the man pages to crle for all the details. But here's a quick howto - how to add /usr/local/lib to the default ls.so.1 path. Run crle with no arguments to see the default paths.

mad[~] crle

Default configuration file (/var/ld/ld.config) not found
 Default Library Path (ELF):   /lib:/usr/lib  (system default)
 Trusted Directories (ELF):    /lib/secure:/usr/lib/secure  (system default)

Use crle -u -l /usr/local/lib to add /usr/local/lib to the default ld.so.1 path.

mad[~] sudo crle -u -l /usr/local/lib
Password:
mad[~] crle

Configuration file [version 4]: /var/ld/ld.config 
 Default Library Path (ELF):   /lib:/usr/lib:/usr/local/lib
 Trusted Directories (ELF):    /lib/secure:/usr/lib/secure  (system default)

Command line:
 crle -c /var/ld/ld.config -l /lib:/usr/lib:/usr/local/lib

And that's it really. The configuration is stored in /var/ld/ld.config but crle should always be used to manipulate it. Hope that is useful.

08/11/07
prstat can be used instead of top, and is supposedly more robust.

Building GCC on Solaris

2007-06-18T21:18:00.001-05:00

Update: On OpenSolaris 2008.11 I used the following (after having intalled gcc packages from blastwave):

../gcc-4.3.2/configure --with-gnu-as --with-as=/usr/sfw/bin/gas --without-gnu-ld --with-ld=/usr/ccs/bin/ld --enable-shared --enable-languages=c,c++,objc,fortran --with-mpfr=/opt/csw --with-gmp=/opt/csw --with-libiconv-prefix=/opt/csw --prefix=/usr/local && gmake -j4

I got a new laptop (my old one was 2 1/2 years old, huge, and prone to overheating - but other than that still not a bad machine). The new laptop is a Dell Inspiron E1505N, shipped with Ubuntu. I removed Ubuntu immediately as my experiences have never been good with it. Vista was installed and removed the next day as well. I'm now happily running (for the most part) Windows XP 64 edition and Solaris Developer edition on the machine. Perhaps a full review of Solaris will be in order later, but for now, I wanted to show how to build GCC 4.2.0 on Solaris.

It is rather simple once you know the tricks.... I leave it to the reader to deduce why all this works, as much of it was just trial and error. Note: I never got gcj to work and I didn't bother with ada. There were several bugs in boehm-gc with which I ran out of patience. Please let me know if you have better success =) I'm new to Solaris still; I've primarily been a user of Linux for the past few years.

Here is the path that was used to build GCC:
bash-3.00$ echo $PATH
/usr/ccs/bin/amd64:/usr/ccs/bin:/opt/csw/gcc4/bin:/usr/local/bin:/opt/csw/bin:/usr/bin:/usr/openwin/bin:/usr/ucb

export LD_LIBRARY_PATH=/opt/csw/lib
(make sure you have mpfr and gmp installed - I installed the packages from blastwave)

And the command to build:
../gcc-4.2.0/configure --with-as=/opt/csw/bin/gas --with-gnu-as --with-ld=/usr/ccs/bin/ld --without-gnu-ld --enable-threads=posix --enable-multilib --enable-nls --with-included-gettext --with-system-zlib --with-mpfr=/opt/csw --with-gmp=/opt/csw --enable-languages=c,c++,objc,fortran --enable-shared --with-libiconv-prefix=/opt/csw && gmake -j 4

The result:

bash-3.00$ gcc -v
Reading specs from /opt/csw/gcc4/lib/gcc/i386-pc-solaris2.8/4.0.2/specs
Target: i386-pc-solaris2.8
Configured with: ../sources/gcc-4.0.2/configure --prefix=/opt/csw/gcc4 --with-local-prefix=/opt/csw --with-gnu-as --with-as=/opt/csw/bin/gas --without-gnu-ld --with-ld=/usr/ccs/bin/ld --enable-threads=posix --enable-shared --enable-multilib --enable-nls --with-included-gettext --with-libiconv-prefix=/opt/csw --with-x --enable-java-awt=xlib --with-system-zlib --enable-languages=c,c++,f95,java,objc,ada
Thread model: posix
gcc version 4.0.2

Zelda: Twilight Princess (Short Review)

2006-12-12T16:31:00.000-05:00

Since I'm lazy, and since people generally like to complain about the bad more than they praise the good, I'm going to follow the norm here. A lot of my points are going to have to do with the wii based controls, so if you played it on the gamecube, I'm willing to bet that your experiences may have varied depending on the situation.

The great: On the whole, I loved playing an action adventure RPG with the Wiimote and nunchuk. In most repsects it is very ergonomic; you can position your hands far or close apart, stretch your arms, and in general just play comfortably. Also, this was definitely a longer game than Ocarina, and in my book longer games are better games (unless they are filled with tedium, but as most Zelda fans know, this is never the case). All of the art work was astounding. The plot may be the best Zelda plot yet, although admittedly the plot is rarely what we are looking for in a Zelda game since we usually know what happens ahead of time, generally speaking.

The not so great: Like any other Wiimote based game, I find it annoying when I want to be extremely lazy and lay down on the couch while I play. I can't complain too much, that's what FFXII and the PS2 are for. Also, I found aiming ranged weapons to be somewhat difficult - partly because my Wiimote receive is high up, and partly because I have a tendency to not steady my arm on my knee (this definitely helps).

The mediocre (mild Spoilers): While most of the boss fights in this game were very entertaining, they weren't really that challenging - at least, I remember Ocarina bosses being quite a bit more difficult in general. The last boss is divided up in to 4 parts, and only one of those parts is really the least bit challenging. The final part (the hardest section in the 4 part fight), had such great potential, but they escaped cheaply by making the boss another block crazy fool, and while it was cool to really use your sword, it would have been nice to have had to use some of the other 8,000 (approx.) items you get in the game. The last fight is really just a trial of patience, much like the cave of ordeals in the game; an hour long endeavor that rewards you with free health potions (the potions also come with an attack boost that lasts about 10 to 15 seconds - hardly worth it in the final fight which is the only time you would use it; this is because most of the time the boss will be blocking your attacks). Warning: limit one per customer.

Really though, this game is hard to beat (in terms of fun, not difficulty...) - I just hope Nintendo cleans up my minor complaints in their next Zelda title, but even if they don't it'll still be great (so long as it doesn't involve more water or air - or space, though I find a Zelda in space to be more unlikely than the analagous Mario Galaxy, than land).