Installation
The installation is the same for all flavors of Unix. The recommended location for Bsoft is in /usr/local. If you want to install Bsoft in a different location, change the environment variable BSOFT to point to the appropriate directory:
setenv BSOFT /usr/local/bsoft
OR
setenv BSOFT $OTHERPATH/bsoft
Copy the distribution file to the desired directory (e.g., /usr/local) and unpack it as follows (it will unpack into a directory named "bsoft"):
Unzip the distribution file and unpack the tar file:
gunzip bsoft1_5_0 .tgz
tar -xvf bsoft1_5_0 .tar
OR
Unpack the gzipped tar file directly:
tar -xzvf bsoft1_5_0 .tgz
All programs are compiled with the C-shell script "bmake" in the main bsoft directory (the -w option prevents display of warnings):
bmake
To avoid compiling the Tcl/Tk interface, run bmake with the following flag:
bmake notcltk
Note on 32 versus 64 bit
Bsoft is 64 bit clean and 64-bit versions should be able to handle large image files (>2Gb). The default on systems capable of both 32 and 64 bit addressing, is 64 bit addressing. To generate 32 bit versions, run the bmake script with the flag "32":
bmake 32
Both 32 and 64 bit versions of Bsoft can coexist by maintaining two separate bsoft directories. When a program is run, the correct version and library for a particular machine will execute, provided that the PATH and LD_LIBRARY_PATH environmental variables are correctly defined. Be sure to distinguish 32 and 64 bit versions of the Bsoft library clearly with the LD_LIBRARYN32_PATH and LD_LIBRARY64_PATH variables under IRIX64.
32-bit only systems: Linux on x86, MacOSX (G4 and pre-Tiger/10.4 on G5, Intel i386), Solaris, VMS, Cygwin_NT (Intel).
64-bit only systems: Linux on Alpha and Itanium, Tru64.
Dual 32- and 64-bit systems: Linux on x86_64, MacOSX Tiger/10.4 on G5 and Intel, IRIX64.
Note on Macintosh G5 and Intel
Bsoft compiled on an Intel Mac generates universal binaries and libraries, each containing four versions: PowerPC 32 and 64 bit, and Intel 32 and 64 bit.
Tcl/Tk on MacOSX
I've packaged the Tcl/Tk applications bshow and brun to be able to launch them from the Finder and the Dock. Run the macinstall script in the bsoft/macosx folder (this requires administrative priveleges). This should install Bshow and Brun in the "/Applications" folder. For every user, copy the .MacOSX directory into their account (e.g., /Users/somebody/.MacOSX). This directory is required to set environmental variables for Finder, and requires a user to log out and back in to be registered by Finder.
Environment
During compilation the script bmake writes two small files called "bsoft.cshrc" and "bsoft.bashrc" with the required environmental variables. The following Bsoft-specific variables are required:
- BSOFT: The main environmental variable pointing to the Bsoft location (usually /usr/local/bsoft)
- BSOFT32: In cases where both 32 and 64 bit versions of Bsoft is required, this variable points to the 32 bit version directory (usually /usr/local/bsoft32)
- BPARAM: This variable points to a directory in the Bsoft tree that includes parameter files for molecular modeling and filter kernels.
The following general environmental variables need to be modified as well:
- PATH: This points to the executable files (usually /usr/local/bsoft/bin)
- LD_LIBRARY_PATH: This points to the directory with the shared libraries (usually /usr/local/bsoft/lib)
Note that there are variants of LD_LIBRARY_PATH, in particular:
- Darwin (Mac OSX): DYLD_LIBRARY_PATH
- IRIX64 (SGI): LD_LIBRARYN32_PATH and LD_LIBRARY64_PATH