Download Bsoft

Version 1.7.0

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  • Unix command line
    
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  • Micrograph pair alignment
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Source code

The gzipped tar archive version 1.7.0 (~11 Mb):

bsoft1_7_0 .tgz

The tar archive version 1.7.0 (~27 Mb):

bsoft1_7_0 .tar

Apart from the major releases, there are development snapshots available. These archives are not necessarily complete and need to be unpacked within an existing bsoft directory.

Platforms supported

• Linux (i386/i686, x86_64, PowerPC, Alpha, Itanium)
  
• Darwin or MacOSX (PowerPC, Intel)
  
• IRIX64 (SGI)
  
• Solaris (Sun)
  
• AIX (IBM)
  
• OSF1 or Tru64 (Alpha)
  
• VMS (Alpha)
  
• Cygwin_NT (Windows NT)

In principle the package could be compiled on any Unix-based operating system.

 

Requirements

Mac OS X:

The default installations of Mac OS X don't have the compilers installed. Download Xcode from the Apple developer's web site and install it first:

http://developer.apple.com/technology/Xcode.html

Note that the Mac OS X versions 10.4 and 10.5+ have different compilers:

• Mac OS X 10.4 (Tiger): Xcode 2.5
• Mac OS X 10.5+ (Leopard and Snow Leopard): Xcode 3+

 

The Z library:

The inclusion of the PNG format in Bsoft requires libz for compression. The required files are:

• /usr/include/zlib.h or /usr/local/include/zlib.h
  
• /usr/lib/libz.* (such as libz.a or libz.so)
  

On some versions of Unix and VMS, libz may not be available, therefore it is included in the distribution and will be compiled.

Tcl/Tk:

Bsoft is primarily a command-line package, with all the necessary code included in the package. However, from version 0.9, it includes a Tcl/Tk interface and a Tcl/Tk script, bshow, useful for the display of images and a few interactive manipulations (not available for VMS). The Tcl/Tk version must be 8.3 or higher. Bsoft can be compiled without Tcl/Tk (see below for details).

On most Unix boxes, the Tcl/Tk headers and libraries are installed in either /usr or /usr/local (look for /usr/include/tk.h or /usr/local/include/tk.h). Linux distributions typically have separate packages for the runtime and developer versions of Tcl/Tk. Both need to be installed to be able to use bshow.

The Bsoft compiler script, bmake, tries to find the Tcl/Tk headers automatically. Make sure the Tcl/Tk version is 8.3 or higher. There may be a version suitable for installation under VMS, but try at your own risk. Make sure the commands "tcl" and "wish" are in your executable path.

 

Enhancements

These enhancements are optional and may be included during compilation.

XML:

The default format for parameter files is the STAR format. These can also be written in an XML format, but requires the libxml2 library with its header files. The common locations for the header files are in /usr/include/libxml2 and the library in /usr/lib. This library is not included in Bsoft due to its sheer size.

OpenMP:

Several operations in Bsoft have been parallelized with OpenMP. Support for OpenMP has been part of gcc since version 4.2, and platforms such as Mac OS X and Linux fully support it.

FFTW3:

Because of the complexities in the new versions of FFTW (3.x), it is no longer included with the Bsoft distribution. It should be compiled as single-precision floating point with support for OpenMP turned on if parallel operations are also desired.

Bernard Heymann 20101117