In case anybody is interested:
I have compiled the current version of NCBI's BLAST package (1.4.9) for
fast sequence database searches under LINUX, using gcc 2.7.2p, optimization
level -O2.
The resulting binaries (in ELF-format) can be downloaded by ftp from
ulrec3.unil.ch in the directory pub/linux/blast
(ftp://ulrec3.unil.ch/pub/linux/blast)
If people at the NCBI are interested in the binary, they might want to
add it to their collection of BLAST executables.
Only few modifications to the source code were necessary. However, finding
them took me a long time...
If you want to do the compilation yourself, here are a few things you may
want to change:
- As documented by the NCBI, use ncbilcl.lnx as the corelib file. The
Makefile works as is, only cc has to be changed to gcc.
- in the 'Gish' part of the package, a modification has to be made to
gish.h in order to enable MMAP. A modified version of gish.h is available
from the above mentioned ftp source. (Maybe all of these MMAP definitions
should go into corelib, anyway)
- The file shmutil.c in the 'gish/misc' directory won't compile on my
linux system since here the 'semctl' function always requires 4 arguments.
On most other unix systems, the 4th one is optional. I am not sure if
it is safe to change the system 'sem.h' file, so I have patched the
shmutil.c and make a copy available on the above mentioned ftp site.
- The kernel you use must have System V IPC enabled.
- for setting up a working BLAST system on a Linux computer, you also need
the auxiliary files which are available from the NCBI ftp-site
ftp://ncbi.nlm.nih.gov/blast
I found the speed of the executables acceptable, on a P166 with a NFS-mounted
database, searches were about 30% faster than on my DEC 3000/400 workstation.
Optimization for Pentium computers did not give any significant speed
improvement, so I switched it off.
I could only test the executables on my own computer (P166, 16MB) having
Red Hat 4.0 distribution installed. I am not sure if it runs on any other
computer, so use it at your own risk.
good luck!
Kay
-------------------------------------------------------------------
Kay Hofmann Tel. +41 (21) 692-5892
Bioinformatics Group FAX +41 (21) 652-6933
ISREC
CH-1066 Epalinges s/Lausanne
Switzerland E-mail: khofmann at isrec-sun1.unil.ch
