Just another quick-post here (as I do not want to go through yet another registration process to leave a single comment in a somewhat silent thread). Also, this may be limited to working on my system. No warranties, support, etc.
As I have installed the Oracle JDK rather than IcedTea (incompatible with some other applications I use frequently), I've first downloaded Java3D from oracle. Currently available from here on the Oracle site. I'm running a 64-bit system, so I chose the -amd64 version, which works fine on Intel - the amd bit is a bit of a misnomer. When I mention java-3d.bin below, I mean whatever file you just downloaded).
First, completely exit MeV (including the small two-line window that I always forget about). Save your work first, if you want to get back to it. Make a backup of the original java3d files (in the lib subfolder, j3dcore.jar, j3dutils.jar, vecmath.jar) that shipped with MeV (or not, if you're happy to reinstall if anything goes wrong).
Open a terminal in the directory that you downloaded java-3d.bin. Then, make the downloaded .bin file executable (chmod +x java-3d.bin). Next, run the file (./java-3d.bin) and decide whether you agree with the license. If you do agree, the programme will extract a number of files in a subfolder of the current directory called 'lib'. Copy or link the three files in lib/ext to the lib/ folder of the MeV installation. Copy the file in /lib/amd64/ to the same folder as the other three files. Restart MeV. Load data. Try viewing/creating a 3D view. Works for me.
Friday, February 14, 2014
MeV and Java 3D in linux
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Wednesday, November 14, 2012
Quick Note: genewise and glib
I've been trying to set up genewise for use with CEGMA, which turns out not to be the most straight-forward setup I've had to do. I'm compiling genewise 2.4.1 on Opensuse 12.2. There are some hints how to get this going on Ubuntu here, but installing glib1 is not an option for me. I can get it to compile and provide sane looking output for the (few) examples I tested as described below.
No guarantee that this works (properly, or at all):
I'm assuming the source has been downloaded and unpacked (and that the required packages for compiling source are present). Go to the src/ subdirectory of the inpacked wise2.4.1 source. To fix the problems described on the page linked above (conflicting types for ‘getline’ and undefined reference to `isnumber'):
sed -i.old 's/getline/getline_new/' HMMer2/sqio.c
sed -i.old 's/isnumber/isdigit/' models/phasemodel.c
To get genewise to compile using glib2 (the whole glib-config not found and glib.h: No such file or directory errors), do (two commands, one line each):
find ./ -type f -name "makefile" -exec sed -i.old 's/glib-config --libs/pkg-config --libs glib-2.0/g' "{}" +;
find ./ -type f -name "makefile" -exec sed -i.old 's/glib-config --cflags/pkg-config --cflags glib-2.0/g' "{}" +;If you tried to compile before, run make clean first. After this run make all to compile. Running make test does not work for me, but manually running some tests does work. Don't forget to set the WISECONFIGDIR variable for your shell!
I don't have time to extensively test this now, so be warned.
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Friday, January 29, 2010
Getting Bio::DB::Sam and samtools working on openSUSE 11.2
The makefile in the samtools package needs some minor modifications in order for this setup to work. Unpack the samtools source package and open Makefile in your favourite editor.
Change the CFLAGS line to read:
CFLAGS= -g -Wall -O2 -fPICDepending on your system architecture you may want to make additional changes there. The above change is likely to be necessary to get the Perl modules to compile.
Further down in the file change the libcurses implementation -lncurses:
LIBCURSES= -lncursesThis is required as SUSE uses as different curses implementation than samtools expects. Next make the samtools package by executing make when in the source directory. (The rest of this document assumes you're working in your favourite terminal application). If you compiled the source before or aren't sure issue a 'make clean' first.
make clean && makeIf you want easier acces to the executables remember to copy samtools and razip to a folder that is included in your path (like ~/bin/ (just you) or /usr/bin/ (system wide)). Now the relevant Perl modules can be installed. Open a Perl shell:
perl -MCPAN -e shell...and then install the relevant module.
install Bio::DB::SamIf all goes well, the module should compile nicely. If you tried to compile the module before you may have to clean out the build directory first. (q to quit the Perl shell).
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Sunday, May 03, 2009
Quick mini-howto: SMS via Skype on Linux (opensuse)
There's a nice description on how to get access to Skype SMS on a linux system running a Skype linux client here. This guide is for Ubuntu, but it works for OpenSuse as well, with a tweak. After extracting skysentials an attempt to run this package will result in:
/usr/bin/python2.5: bad interpreter: No such file or directoryTo get around this, open skysentials.py with your favourite text editor and change the very first line from:
#!/usr/bin/python2.5to:
#!/usr/bin/python...and it should work.
Bonus: if you want an easy link to the script, put the folder containing the files somewhere where it's not in the way and create a symbolic link in the 'bin' folder in your home directory:
ln -s /path/to/skysentials.py ~/bin/skysentials...where you can also opt for another name and /path/to/skysentials.py should be the full path pointing to the skysentials.py script that you just saved.
This will allow you to just type skysentials from any terminal or run dialogue, without having to specify the full path or browse to the folder. E.g.: if you're using KDE, hit Alt+F2 to bring up a run dialogue, type skysentials and hit enter.
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Sunday, January 25, 2009
Quick mini-howto: OpenSuse11.1 OpenOffice Impress TwinView Presenter Console 64bit
The insanely long title is required as I've experienced that all mentioned items contribute to the issue of the whole setup not working. If you're using OpenSuse's 11.1 version of OpenOffice with an Nvidia (binary driver from the repo) TwinView setup and want to run a presentation on the external monitor you'll find it doesn't work. The multiple monitor section in slide show settings is grayed out. Oddly enough this does work with the packages directly from Sun. I'm assuming that TwinView is already properly set up.
- uninstall all openoffice packages from openSuse (search for openoffice, select package > all in this list > delete).
- download the relevant openoffice package from Openoffice.org (other systems). I'm using the linux 64 rpm without Java JRE, which you get by unchecking the checkbox above the table.
- create a folder to hold the installer files, move the installer file there and unpack it (on the command line 'tar -xvpf
') - Add this folder to your repositry list (in the software manager Configuration > Repositories). Click 'add', select 'local directory' give it a name, point to its location and specify that it is a 'plain rpm directory' by checking the checkbox under the line where the location is specified.
- Apply the changes, search for OpenOffice and install what you need. Check with the version tab whether you've selected the version from the local rpm directory and not the repository version. If you have the files for both the i586 and the x86_64 version in the directory (like I accidentally had), check whether the x86_64 will be installed for all packages, as by default it seems to create a random mix.
- Also select the OpenOffice_org-ure package from the repositories. I needed the repository version to get the presenter console working.Optionally this step can be delayed until the Sun Presenter Console is installed (see step 9 if the presenter console ends up not working). Apply all the changes.
- Download the Sun Presenter Console (in my case the linux x86-64 version towards the bottom of the list). Save it somewhere on your system. You can try adding it directly by opening the file with openoffice, but likely it will complain that the extension 'Sun Presenter Console' doesn't work on this computer. If it does work fine, you're done. If not:
- Unzip the package (the .oxt file you downloaded) (command line 'unzip
') and fire up your favourite editor to edit the file description.xml. Two things need to be changed: the tag that lists 'identifier value' and the tag that lists 'platform value'. Both should contain 'linux_x86', which should be 'linux_x86_64'. - Optionally check that the required libraries are present: in a terminal run 'ldd PresenterScreen.uno.so' and check whether the output complains about any missing files. If there are some files missing you probably didn't install the OpenOffice_org-ure package from the repositories.
- Zip the package back to an .oxt file (or zip and rename to .oxt) (in a terminal 'zip -r sun-presenter-console-fix.oxt *')
- Open the new .oxt file with openoffice and it should pop-up with a dialogue about adding the extension. Installation should procede normally and after installation the presenter view should pop-up when you've configure a presentation to run on a specific monitor via the slide show > slide show settingsmenu.
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Labels: mini-howto
Sunday, November 16, 2008
Windows Vista Revisited
- Suse: not all my hardware works straight away. An nvidia driver that didn't support my graphics card (too new) was automagically installed and caused by screen to wipe out as soon as X started. The touchpad doesn't work when I'm docked, with another mouse attached. The display problem was solved in the next update to Suse.
- Windows: Switching the dock on when windows is on (forgetting to plug it in) crashes windows to oblivion (blue screen of death). Linux happily keeps on running, telling me the adapter is now plugged in, activating my mouse and periferals.
- Suse: multiple screens and linux still don't play nicely together.
- Windows: Some multi display settings are now arcane to set; half of the options were grayed out in one place, but not in another.
- Windows: After upgrading my RAM it told me I needed to buy a licence for windows, as my hardware had changed. (I have a removable cdrom drive and docking station. Aparently this presents windows with too many hardware configurations and it decides to deactivate itself as a result).
- Windows: Whilst trying to copy a lab audio CD (no protected content); I'm sorry dave, I can't do that. Linux happily rips the cd to disk and asks me how many copies I want to burn. This is Vista's DRM at work.
There's a very in-depth story about why Vista DRM and related 'features' suck here: A cost analysis of Windows Vista content protection.
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Tuesday, November 04, 2008
A Quick note on Cell press RSS feeds
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The Kodak EDAS 290 and WinXP
The kodak EDAS290 imaging machine we use at the lab (with Kodak 1D software) was recently migrated to a new computer running Windows XP. Windows could see the camera, the camera works, but the software insists the camera is nowhere to be found. The problem and solution are as follows: the driver that windows XP automatically uses for the camera isn't supported by the 1D software. The driver files are located in the program files directory under 'common files' and then somewhere under 'kodak'. Telling windows to use the driver can be done by selecting 'update driver' under properties of the kodak camera (under 'imaging devices' in the hardware manager) and choosing 'I will select the driver to install' (or, look for driver and specify the location, fiddle around a bit under the directory mentioned above to find the exact location). Two drivers show up on our system: the one that has a name slightly different from the current name is the correct one (I think it has the word 'zoom' in the title). Installing the correct driver should cause a direct detection of the camera, and restores functionality of the software.
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Thursday, July 24, 2008
The short update
My thoughts on:
- US customs (entry) - I AM NOT A MEDICAL STUDENT!, other than that people are polite and efficient. Less questions asked than when leaving europe, just more often (4x, iso once).
- The US - Can I have an extra extra small please?
- US customs (exit) - So... where do I leave? Wait, I already left?
- That car commercial - It needs to look like a parking meter because otherwise people won't find it - it's supposed to look like one, you idiots! And why does the car you're selling look just like any other car?
- How to waste the next couple of minutes:
- Number watch, especially everything that gives you cancer, according to epidemiologists.
- The fines levied for the nipplegate incident were recently overturned. But fear not, not all black bar measures have been abolished: The BPA - Toe Jam (Music Vid).
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Thursday, May 01, 2008
Now why doesn't IKEA sell...
... tables like this interactive coffee table? Yours for only $2000 here (or, if you like soldering, the kit costs $400 here, excluding furniture).
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Friday, April 25, 2008
A quick note to Phorm
Regarding your recent criticism of the FIPR (here), I would just like to add the following:
- Regardless of what the agenda of the FIPR is, they do have a point that the Home Office advice does not prove the legality of the system. Evasiveness in answering to legality concerns is doing more damage than the FIPR can ever do on its own.
- The fact that an organisation is legit, does not imply that all its activities are legal. The question whether something should be legal, is a separate question which is for the law makers to decide on.
- The way in which internet users are better served is not determined by you, the ISPs, or any commercial party. This is determined by the users themselves. These users have a right to be informed about matters that concern decisions in this regard. Independent foundations such as FIPR serve a crucial role to provide balanced information on such matters and, even more so, on the consequences of such matters. Furthermore, relevant information is currently not being provided in an adequate manner by you (and BT for that matter), supporting the need for an organisation that does not have a commercial goal driving their agenda.
- The FIPR does not wish to block technological process, it wishes to block technological process that has negative consequences or that has not sufficiently been tested. In the natural sciences and especially in the medical sciences there are many ethics and safety commissions that safeguard against implementation of technological processes that may be harmful or potentially unsafe. Though these consequences are often physical damage, damage to social values and structures, including privacy, are arguably of equal severity. In this regard the FIPR is not abusing its influence, it's merely doing what it should be doing.
- I have taken notice of your arguments for using your services and even without the FIPR's standpoint I am not convinced of why such services are desirable for me. I do find that many of my concerns are not addressed in your information, making it impossible to reach a valid informed choice about the service based on your information. In this regard the FIPR is doing just that which you claim it is standing in the way of doing: allowing me to reach a valid and informed choice.
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Monday, March 24, 2008
Hoax of the week: Pope Goestheveezl
Half a pound of treacle
That's the way the chimney smokes
Pope Goestheveezl
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Wednesday, March 12, 2008
More Microsoft annoyances...
Linux 2, Microsoft 1 --- Time to catch up Microsoft, decision time is approaching fast!
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Tuesday, March 11, 2008
Sins updated
Of course, there's always a third option: people will leave the (already rapidly shrinking) church altogether and join a protestant church, or go their own way.
Nobody expects the Spanish inquisition!
*I wonder when the Vatican is going to hand out money, it seems they have plenty of cash to spare...
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Sunday, March 02, 2008
My faith in Microsoft is quashed, again.
Windows vista home basic came pre-installed, and, out of curiosity I acquired a copy of a vista ultimate update cd bundled with office 2007 via my university. I'm also used to running linux on my machines, and the server I use at the university (which I also maintain) runs unix, so it's always going to be a battle between OSes on my machine. Windows had just scored major points (as it always does) for handling multiple monitors better than the competition, and lenovo (laptop manufacturer) had won points for integrating their (useful!) apps nicely with Vista, indirectly adding point to the windows score. Windows had lost point for not having a customisable install and taking 40Gb of diskspace, whilst linux took less than 6 whilst still having all the functionality that I need.
Then I changed my memory (from 2Gb to 4Gb), which windows 32 bit can't fully recognise, but the tools that really need it are linux-only anyway, so that's why there's double boot). No problems. Two weeks later this script plays out:
[Vista]: *DING* Windows has detected a hardware change and needs to be reactivated.
[Me]: WT*? Okay, I'll play along, "Activate Windows!" *clickety*...
[Vista]: ...*DING* This product key is already in use. You need another key to activate windows!
[Me]: WT*^2?
[Vista]: Click here to buy a new one!
[Me]: WT*^3!!!
[Vista]: Call the automated phone system to activate windows...
[Me]: Hmmm, maybe they have a 'press 9' for a real person if registration fails.
[Skype]: This is an invalid number. (The toll free number)
[Me]: WT*?, tries non-toll free number
[Product activation]: (Long story with lots of numbers as input)
[Me]: Plays along, hits next after entering whole lot of numbers.
[Vista]: Registration succesfull, have a nice day!
[Me]: WT*^27.5
MS source: Windows Vista Activation Hardware Change see the bit about "What hardware changes may require re-activation". I don't have time for this stuff, I'm supposed to be working as a PhD student...
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Thursday, February 21, 2008
Hoax of the week: RCAM / Joseph Chikelue Obi
The above is true, it's no hoax (plenty of other blog entries and an overview here at the register), but in my personal opinion the RCAM deserve an entry as "Hoax of the week".
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Sunday, November 04, 2007
Jumping to incorrect conclusions pt.1
There's a study entitled "Depression among Adults Employed Full-Time, by Occupational Category" over here. Very nice to see that 'Life, physical and social science' is near rock-bottom when it comes having been depressed between 2004 and 2006. The only happier bunch of people are those working in "Engineering, Architecture and surveyors". The last table shows that both males and females are happiest in 'Life, physical and social science'. Hold on, they score lower in the overall score table. Now let's jump in a completely scientifically incorrect manner: For these lines of work, it doesn't matter what you do, as long as there aren't too many women around to make you depressed. If you take the numbers of the two mentioned categories, you can work out that the ration men:women is. For the sciences it's 1.3:1 and for the Architects etc it's 6.8:1. Fewer women, lower overall depression rate. But why not the other way round? Are the men depressing the women and driving up the female depression rate, compensating the fact that there are less of them? No, there are no men in "Personal care and Service" and still women have a depression rate higher than the depression rate of males in any occupational category...
And that's how to draw completely wrong conclusions (on my part) based on what might be valid data (haven't looked into it that well).
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Wednesday, October 31, 2007
Cars, fuel & the environment
So, as usual: we're all doomed. If it isn't that comet that's heading for earth and is expected to pass within lunar orbit in 2036 that finishes us off, it'll be our own doing in the form pollution beyond repair. Now, I'm not saying we shouldn't be watching the environment - I'm just not convinced that what's being done makes sense. The following are all thoughts on comments made in the media, or recent popularised developments.
First off: The cars, but more importantly, the trucks themselves. Recently there was news coverage of a trucking convention - a show where the latest developments in trucks were showcased. It featured a hydrogen truck, and a hybrid truck. Both of them weren't too popular (yet) and a critic mentioned that it was all show anyway - nothing ever changes and trucks were the most polluting vehicles on the road, using 1 litre of fuel to travel 3 km (1:3). This is, of course, a bad argument as to why they are so polluting. Say a truck carries 25 tonnes of freight, and a car can carry half a tonne (crude estimates). If you have a very fuel-economical car it might do 1:25 (optimism ain't dead yet). To carry 25 tonnes, you need 50 cars, which would be equivalent to a single vehicle doing 1:0.5. In other words: a truck is more efficient than a car.
Hybrid cars and especially hydrogen vehicles, combined with new plans by Dutch ministers, do solve overcrowding problems in the Netherlands. A large percentage of cyclists has no clue about traffic safety, and many use headphones on the bike. Combine this with very silent tires (the ones that NL wants to make compulsory) on silently running electrical cars...
In the above rant fuel already features a prominent role. But there's more. Hydrogen is all nice and dandy, but it is only used as an energy store (as any fuel is merely a store). The question is: where do you get the energy from to create hydrogen? If you're burning fossil fuel to get this energy, you're just geographically shifting the pollution. So aside from the fact that hydrogen is hard to come by at present - it also requires a large investment in durable energy.
One source would of course be solar energy (according to pop-sci channels the earth takes up 8 times more energy then we need on earth - although I wonder how much we need to keep the earth warm). One way of harnessing this power is by - well let nature do it for you. Grow plants, harvest plants, convert energy stored in sugars within the plants. In most cases this is done by converting sugars to ethanol, which burns well and can be used to power vehicles. Brazil started a huge biofuel project in the 70's, and it's still running. They use sugar cane. The US uses corn, and went from no usage to moderate usage overnight. The corn price tripled overnight, meaning that in countries like mexico the poor could no longer afford their food and the meat prices doubled on their own market. Also, the way that it's being grown and refined, may actually cause more pollution and may cost more energy than it's yielding. This is certainly the case for palm oil, a lot of which comes from Indonesia. The problem here is that the land on which the palms are being grown are being cleared by burning down the natural forests of the country. As far as carbon emissions go, this is worse than traffic.
As a final, not so directly related note: Discovery Channel is opting for the 'most of us will be dead soon anyway'-approach. Their future cars programme is advertised with a short that acts as if it's selling a car to you. You being number 48095 or something 5 digit like. Seeing as they indicate a globalised economy (the car is 2 million credits) you'd expect that ID numbers would also be global. In other words - they don't expect more than 100000 registered people by then. I guess that'll turn out to be the most interesting future vision the programme will have on offer.
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Sunday, October 07, 2007
The most confusing one yet...
In other words: I can barely comprehend why anyone would use the above argumentation at all - all it achieves with me is that I'm less inclined to give any other arguments put forward by the same speaker any thought.
IKEA-ism not your thing? Unconfirmed reports (Guinness World Records) mention that the Bible is the most sold book (the IKEA catalogue is free!) and somewhere else is mentioned that the Red book comes in second. Where the Qu'ran and other scriptures fit in, I don't know... As for believing the 'old and wise', I don't know which is referenced first, the Bible, or the Kama Sutra.
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Sunday, September 30, 2007
Back from the UK
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