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: [EMAIL PROTECTED]
*/
