mpiblast 的安装与运行.docVIP

Installation for Unix/Linux/BSD If you are using Linux on Intel or AMD hardware, you may be able to find a pre-compiled RPM of mpiBLAST from Scalable Informatics. Otherwise, you will have to download and compile mpiBLAST from source code. There are five steps to installing mpiBLAST from source. Install MPI (if not already installed) Download and extract mpiBLAST and the matching NCBI Toolbox release Patch and compile the NCBI Toolbox Compile and install mpiBLAST Configure mpiBLAST by editing the ~/.ncbirc file Each of these steps are described in more detail below. 1) MPI installation Two popular free versions of MPI are MPICH and LAM/MPI. A successful installation of either is sufficient for mpiBLAST to work. Many OS vendors bundle either MPICH or LAM-MPI with the system, making an installation from source unnecessary. 2) Download and extract mpiBLAST and the matching NCBI Toolbox release 2a) Download mpiBLAST from Downloads.Archive.html.html. wget /downloads/files/mpiBLAST-x.y.z.tgz or wget /downloads/files/mpiBLAST-x.y.z.tbz 2b) Extract mpiBLAST tar -xvzf mpiblast-x.y.z.tgz or tar -xvjf mpiblast-x.y.z.tbz 2c) Download the NCBI Toolbox from /toolbox/ncbi_tools/. (Note: mpiBLAST-1.4.0 requires the October 2004 release.) wget /toolbox/ncbi_tools/oldncbi.tar.gz 2d) Extract the NCBI Toolbox tar -xvzf ncbi.tar.gz 3) Patch and compile the NCBI Toolbox In order to provide exact e-value statistics, mpiBLAST requires slight modifications to the NCBI Toolbox. We have provided a patch that modifies the NCBI Toolbox accordingly. Once patched, the toolbox must be re-compiled prior to compiling mpiBLAST. The e-value patch is required for mpiBLAST to work properly. 3a) Change to the directory containing the NCBI Toolbox cd /path/to/ncbi (most likely the command will simply be cd ncbi) 3b) Apply the patch distributed with mpiBLAST patch -p1 /path/to/mpiBLAST-x.y.z/ncbi_Oct2004_evalue.patch  Output should look like: patching file tools/bl