NCBI C Toolkit Builds: Initial Test Install on a new UNIX/Linux system (Updated Jan 2011) MacOS X Instructions Page IllumOS Instructions Page
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-c++ 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.
on Zypper compatible systems (OpenSUSE) zypper install gcc gcc-c++ flex make zypper install openmotif-devel freeglut-devel ncurses-devel termcap on Debian-based systems: (these are tested on Ubuntu 10.10) apt-get install csh apt-get install g++ apt-get install flex apt-get install libmotif-dev apt-get install freeglut3-dev apt-get install libncurses5-dev apt-get install libpng12-dev apt-get install x11proto-print-dev apt-get install libxmu-dev apt-get install libxft-dev apt-get install libfontconfig1-dev apt-get install libjpeg8-dev apt-get install libxp-dev BioSLAX is using slapt-get instead of apt-get
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 and OpenSUSE these are all shared libraries, not .a files)
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: 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
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) SEE THE ATTACHMENTS BELOW FOR WORKING COPIES OF THE LINUX makefiles for 32-bit CentOS/Fedora (linux-x86.ncbi.mk) and 64-bit CentOS/Fedora (linux.ncbi.mk) Copy these into the ./ncbi/platform directory overtop the older non-working variants.
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.
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Christopher Hogue's Research > RCE in Mechanobiology Advanced Bioinformatics Software Development Workshop >