[gentoo-science] ncbi-c++ toolkit

[gentoo-science] ncbi-c++ toolkit

[Davide Cittaro]

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Hi all, I would like to share some info on NCBI C++ toolkit for a  
possible ebuild.
Actually I'm not practical with writing complex ebuilds (I'm going to  
explain why later). BTW I succesfully compiled NCBI C++ toolkit in  
this way:

I modified the configure script:

$ diff -Naur configure configure.orig
--- configure   2006-12-04 11:58:09.000000000 +0100
+++ configure.orig       2006-12-04 11:52:44.000000000 +0100
@@ -20602,20 +20602,16 @@
## NCBI C Toolkit
if test "$with_ncbi_c" != "no" ; then
-   NCBI_C_PATH=${NCBI_C_PATH:="/usr"}
-   #NCBI_C_PATH=${NCBI_C_PATH:="$NCBI"}
+   NCBI_C_PATH=${NCBI_C_PATH:="$NCBI"}
     if test "$ncbi_compiler" = ICC -a -d "$NCBI_C_PATH/ncbi_icc"; then
        NCBI_C_PATH=$NCBI_C_PATH/ncbi_icc
     fi
-   NCBI_C_INCLUDE="-I$NCBI_C_PATH/include/ncbi"
-   #NCBI_C_INCLUDE="-I$NCBI_C_PATH/include${bit64_sfx}"
+   NCBI_C_INCLUDE="-I$NCBI_C_PATH/include${bit64_sfx}"
     if test "$with_debug" = "no" ; then
-     NCBI_C_LIBPATH="$NCBI_C_PATH/lib"
-     #NCBI_C_LIBPATH="$NCBI_C_PATH/lib${bit64_sfx}"
+     NCBI_C_LIBPATH="$NCBI_C_PATH/lib${bit64_sfx}"
     else
-     NCBI_C_LIBPATH="$NCBI_C_PATH/lib"
-     #NCBI_C_LIBPATH="$NCBI_C_PATH/altlib${bit64_sfx}"
+     NCBI_C_LIBPATH="$NCBI_C_PATH/altlib${bit64_sfx}"
     fi
     if test "$with_mt" = "yes" ; then
       NCBI_C_LIBPATH="$NCBI_C_LIBPATH $NCBI_C_LIBPATH/ncbithr.o"

This modification was necessary because gentoo puts NCBI C libraries  
and headers in places where the C++ toolkit doesn't expect.
I ran configure with these args:

$ ./configure CXXFLAGS=-fexceptions --prefix=/opt/sci-biology -- 
host=i686-pc-linux-gnu --with-mt --with-algo --with-bin-release -- 
with-lfs --with-autodep --with-python=/usr --with-fltk=/usr --with- 
sqlite3=/usr --with-ctools --without-debug  --without-xerces -- 
without-xalan --without-gui

I've edited Makefile.mk (located into GCC411-ReleaseMT/build)  
deleting -fno-exceptions in

MYSQL_INCLUDE = -I/usr/include/mysql -pipe -ffast-math - 
DHAVE_ERRNO_AS_DEFINE=1 -fno-exception -fno-strict-aliasing

row, otherwise it doesn't compile (I believe this depends on how one  
compiled mysql...)

and

$ make

This is a complex ebuild to me because blast* commands are provided  
by this toolkit, and they possibly conflict with the ones provided by  
ncbi-tools. It would be nice to have both installation in slot and  
select one or the other with eselect (at least blast* commands).

cheers

d
/*
Davide Cittaro
HPC and Bioinformatics Systems @ Informatics Core

IFOM - Istituto FIRC di Oncologia Molecolare
via adamello, 16
20139 Milano
Italy

tel.: +39(02)574303007
e-mail: davide.cittaro@ifom-ieo-campus.it
*/



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