31 Oct 2009

NCBI C Toolkit Builds: Initial Test Install on a new UNIX/Linux system

 

Unix build farm systems should be installed with full X11R6 (Xwindows) support.

OpenMotif, FreeGlut  and Ncurses libraries are needed to build Vibrant applications like VisTraj.

 

STEP 1

 Configue your Unix/Linux system with necessary compilers, tools and libraries 

As root: Check to see if compilers (at least gcc) are present – install these as required.

On YUM compatible Linux systems the following packages are needed (Centos 5.4 or Fedora Core 12):

yum install gcc

yum install gcc-c++
yum install flex

yum install imake.i386 (or .i686 ...)

yum install openmotif-devel.i386 (for Fedora Core 12, try lesstif-devel.i686)

yum install libXmu-devel.i686 (FC 12 only)

yum install freeglut-devel.i386 (or .i686 ...)

yum install tcsh (FC 12 only)

yum install libpng10-devel.i686 (FC 12 only)

yum install ncurses-devel.i386 (or .686 ...)  

Ensure you can compile a test C and C++ program (hello world) on the system before proceeding.

 

STEP 2

Know where Motif libraries are, and ensure OpenMotif header files are in place.

IF LOCATIONS ARE DIFFERENT – WRITE THEM DOWN HERE.

 

Find where the system keeps its X11 libraries and *.h files:

cd /

find . -name "libXm.a" -print

 

i.e. on CentOS 5.x these are in

/usr/lib

(On FC 12 these are all shared libraries, not .a files, loaded with lesstif)

 

cd /

find . -name "X.h" -print

i.e. on CentOS 5.x these are in

/usr/include/X11/X.h 

 

other systems may use version tags:

/usr/X11R6/include

/usr/X11R6/lib

 

ALTERNATIVELY try this set of commands to initialize and lookup file locations:
updatedb

locate libXm

 

Once you have found a library file – you can report its version number as follows: 

strings /usr/X11R6/lib/libXm.so.4.0.0  | grep -i version

 This will reveal either Motif Version or GNU/Lesstif Version strings
e.g.  Motif Version 2.3.1 or GNU/LessTif Version 2.1 Release 0.95.2

Check to see if GLUT is installed

cd /

find . -name "glu.h" -print

 i.e. on CentOS these are in

/usr/include/GL

Check to see if PNG libraries/headers are installed

cd /

find . -name "png.h" -print

 i.e. on FC12 these are loaded with YUM and put in

/usr/include/libpng10

but on CentOS these are in

/usr/include

 

Eclipse for C, C++ and Java may be installed.

 Explore with YUM and find the eclipse C development package to install

STEP 3: TEST COMPILE THE NCBI Toolkit as downloaded from NCBI

 

Install NCBI toolkit - into /usr directory

as root

cd /usr

ftp ftp.ncbi.nlm.nih.gov/toolbox/ncbi_tools/ncbi.tar.gz

 

Then uncompress and untar the file with:

gunzip ncbi.tar.gz

tar –xvf ncbi.tar.gz

 

This will create a /usr/ncbi directory 

 

(OPTIONAL for some UNIX variants: As per NCBI instructions, may need to edit the makefile in the ./ncbi/platforms directory to point to the directories you found on the previous page for libraries and header files) 

 

Complile NCBI toolkit and ensure that it builds properly

To execute the build - as per instructions:

./ncbi/make/makedis.csh 2>&1 | tee out.makedis.txt

 

examine the file

out.makedis.txt

and look for errors - remedy if necessary.

ERRORS usually indicate missing packages.

Go over the YUM list at the top and make sure all these packages are installed.

Other errors may need changes to the make file in the /ncbi/platform directory

(the makefile used for FC 12 is attached below)

 

examine the directory

/usr/ncbi/lib  - it should have the following 27 libraries present:

libblast.a

libblastapi.a

libblastcompadj.a

libddvlib.a

libncbi.a

libncbiacc.a

libncbiCacc.a

libncbicdr.a

libncbicn3d.a

libncbicn3dOGL.a

libncbidesk.a

libncbiid1.a

libncbimla.a

libncbimmdb.a

libncbiNacc.a

libncbiobj.a

libncbitool.a

libncbitxc2.a

libnetblast.a

libnetcli.a

libnetentr.a

libregexp.a

libvibgif.a

libvibnet.a

libvibrant.a

livibrantOGL.a

ncbithr.o

 

If the OGL libararies are missing (libvibrantOGL.a and libncbicn3dOGL.a)

- this is because GLUT is not installed or specified properly in the makefile.

Ensure libraries for Motif  and Glut are present.