MeV and Java 3D in linux

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.

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.

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 -fPIC

Depending 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= -lncurses

This 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 && make

If 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::Sam

If 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).

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 directory

To get around this, open skysentials.py with your favourite text editor and change the very first line from:

#!/usr/bin/python2.5

to:

#!/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.

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.

1. uninstall all openoffice packages from openSuse (search for openoffice, select package > all in this list > delete).
2. 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.
3. create a folder to hold the installer files, move the installer file there and unpack it (on the command line 'tar -xvpf ')
4. 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.
5. 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.
   
6. 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.
   
7. 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:
8. 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'.
9. 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.
10. Zip the package back to an .oxt file (or zip and rename to .oxt) (in a terminal 'zip -r sun-presenter-console-fix.oxt *')
11. 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.