[BioC] Affymetrix gtype_cel_to_pq

[Cawley, Simon]

Hi Henrik,

Apparently the Makefile didn't make it to the tarball we posted - that was a mistake.  We'll repost, in the meantime find it included below.  It has been compiled and tested on linux (on both i386 & amd64 processors).  Should work on other platforms too, though we haven't tested.

-S

------------------BEGIN MAKEFILE----------------------
#
# This code requires the Affymetrix FileSDK to compile - it is available from
# <http://www.affymetrix.com/support/developer/filesdk/index.affx>
#
# There are several constants that may need to be defined to enable compilation
# and execution on specific operating systems. These are :
#
# Makefile variables you MUST set:
#    SDK_FILE                 Set to wherever the FileSDK is located.
#    SDK_PORTABILITY          Set to wherever the FileSDK is located.
#
# Compilation variables which you may need to add to the CPPFLAGS variable below:
#    IS_BIG_ENDIAN            Define if the machine represents data in big endian format.
#    _INCLUDE_UNISTD_HEADER_  Define if the UNISTD.H header file is used by your C++ compiler.
#    WIN32                    Define if using the MSVC++.NET compiler.
#    _USE_MEM_MAPPING_        Define if you want to enable memory mapping for BAR, BPMAP, CDF and CEL file reading.
#

SDK_PORTABILITY:=../../../portability
SDK_FILE:=../../../file

CPPFLAGS = -O2 -I $(SDK_FILE) -I $(SDK_PORTABILITY)
# The following line is an example of what you should use on a big endian machine
#CPPFLAGS = -O2 -I $(SDK_FILE) -I $(SDK_PORTABILITY) -DIS_BIG_ENDIAN

CC=g++

SOURCES=\
	$(SDK_FILE)/CELFileData.cpp \
	$(SDK_FILE)/CDFFileData.cpp \
	$(SDK_FILE)/FileIO.cpp \
        hash.cpp \
        gtype_cel_to_pq.cpp

OBJECTS=$(SOURCES:.cpp=.o)

EXE=gtype_cel_to_pq

all: $(EXE)

$(EXE): $(OBJECTS)
	$(CC) $(CPPFLAGS) $(OBJECTS) -o $@

clean:
	-rm -rf $(OBJECTS) $(EXE)

------------------END MAKEFILE----------------------



On Tue, 18 Oct 2005, Henrik Bengtsson wrote:

> Date: Tue, 18 Oct 2005 19:25:16 +1000
> From: Henrik Bengtsson <hb at maths.lth.se>
> To: bioconductor at stat.math.ethz.ch
> Subject: [BioC] Affymetrix gtype_cel_to_pq
>
> Hi,
>
> I need to get hold of Affymetrix' gtype_cel_to_pq in order to use the
> RLMM package.  This is an non-supported tool by Affy and therefore I
> hope someone else can help me out.
>
> Affymetrix provides the (platform independent) C++ source code at
> http://www.affymetrix.com/support/developer/tools/gtype_cel_to_pq/ and
> says "This is the source code for the gtype_to_cel_pq tool. To build
> this application you will also need to download and compile the File
> SDK [http://www.affymetrix.com/support/developer/filesdk/]. The source
> code provided has only been compiled and tested on a Linux system
> using the g++ version 3.3 compiler.".
>
> Has anyone successfully built this tool on Unix, Linux or even Windows
> (Cygwin?) and if so could you please tell me what compile and link
> options you used for g++?
>
> I am aware of Nusrat Rabbee's pre-compile Linux version at
> www.stat.berkeley.edu/users/nrabbee/RLMM/convert.html, but it does not
> run on the Unix system I have access.
>
> Best wishes
>
> Henrik Bengtsson
>
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