[MINC-users] installing brain-view2

[Mishkin Derakhshan]

I had a hell of time installing brain-view2 so I documented my errors
and solutions/hacks in case others come across the same problems
(read: when I have to do this again I can look back at this post).

This was on a ubuntu 12.04 64 bit machine.

I followed the instruction here (thank you jason and sghanavati):
https://wiki.phenogenomics.ca/display/MICePub/brain-view

Pre-requisites
1. MINC. I used the minc-toolkit binaries and only ran into one minor problem.
opus[~]$ sudo apt-get install libc6 libstdc++6 imagemagick perl
freeglut3 libgl1 libxcb1 libxdmcp6 libx11-6 libxext6 libxau6 libuuid1
libjpeg62 libexpat1 libtiff4
Reading package lists... Done
Building dependency tree
Reading state information... Done
Package libgl1 is a virtual package provided by:
  libgl1-mesa-swx11 8.0.2-0ubuntu3.1
  libgl1-mesa-glx 8.0.2-0ubuntu3.1
You should explicitly select one to install.

E: Package 'libgl1' has no installation candidate

I chose libgl1-mesa-glx at random, and then everything else worked.

2. Qt4: sudo apt-get install qt4-qmake libqt4-dev libqt4-core
3. Boost: sudo apt-get install libboost1.48
4.Coin:
wget http://ftp.coin3d.org/coin/src/all/Coin-3.1.3.tar.gz
tar xvzf Coin-3.1.3.tar.gz
mkdir coin-build
cd coin-build/
../Coin-3.1.3/configure
make
sudo make install

5. Quarter:
wget http://ftp.coin3d.org/coin/src/all/Quarter-1.0.0.tar.gz
tar xvzf Quarter-1.0.0.tar.gz
mkdir quarter-build
cd quarter-build/
../Quarter-1.0.0/configure
make

ERROR:../../../Quarter-1.0.0/src/Quarter/Quarter.cpp:148:13: error:
'stderr' was not declared in this scope
SOLUTION:Added
#include "stdio.h"
to this file: ../Quarter-1.0.0/src/Quarter/Quarter.cpp

make
sudo make install

6. HDF5 1.8.9:
Downloaded a build of HDF5 1.8.9:
http://www.hdfgroup.org/HDF5/release/obtain5.html
tar xvzf hdf5-1.8.9-linux-x86_64-static.tar.gz

7. BicInventor:
wget http://packages.bic.mni.mcgill.ca/tgz/bicInventor-0.3.1.tar.gz
cd bicInventor-0.3.1
./configure --prefix=/opt/minc --with-build-path=/opt/minc
--includedir=/opt/minc/include --libdir=/opt/minc/lib --with-minc2
ERROR: (lots of erros when I tried to configure)
SOLUTION: sudo apt-get install build-essential realpath zlib1g-dev
bison flex libx11-dev libxmu-dev byacc libsoqt4-dev automake libtool
libdbi- perl libblas-dev liblapack-dev libblitz0-dev libreadline-dev
bzr bzrtools octave3.2 imagemagick

./configure --prefix=/opt/minc --with-build-path=/opt/minc
--includedir=/opt/minc/include --libdir=/opt/minc/lib --with-minc2
make
sudo make install

ACTUALLY INSTALLING BRAIN-VIEW2
mkdir bv2
cd bv2
git init
git remote add origin git at github.com:sghanavati/brain-view2.git
git pull -u origin master

qmake-qt4 MINCDIR=/opt/minc/
HDF5DIR=/home/mishkin/hdf5-1.8.9-linux-x86_64-static/ brain-view2.pro
make
ERROR: GeometryNode.h:25:30: fatal error: H5Cpp.h: No such file or directory
SOLUTION: sudo apt-get install libhdf5-serial-dev (probably a bad hack
because it installed 1.8.4 but it worked)

ERROR: H5AtomType.cpp:(.text+0x257): undefined reference to `H5Tget_pad'
SOLUTION: put -lhdf5_cpp before -lhdf5 in the g++ command
 g++ -m64 -o brain-view2 MainWindow.o BrainQuarter.o TreeItem.o
TreeModel.o ResourceForm.o GeometryScene.o GeometryNode.o main.o
textureColumn.o textureFileItem.o tagFileItem.o tagPointItem.o
moc_MainWindow.o moc_BrainQuarter.o moc_TreeItem.o moc_TreeModel.o
moc_ResourceForm.o moc_GeometryNode.o moc_textureColumn.o
qrc_colourbars.o    -L/usr/lib/x86_64-linux-gnu -L/usr/X11R6/lib64
-L/usr/local/lib -lCoin -L/lib/ -lQuarter -L/opt/minc//lib -loobicpl
-lpcre++ -lbicpl -lvolume_io2 -lminc2 -L/lib -lbicInventor
-L/home/mishkin/hdf5-1.8.9-linux-x86_64-static//lib/ -lhdf5_cpp -lhdf5
-lQtOpenGL -lQtGui -lQtCore -lGL -lpthread

And that gave me the brain-view2 binary which i copied into /opt/minc/bin.