BIRCH
BIRCH - Install FASTA packages

Install the FASTA packages

The COPYRIGHT agreement for the FASTA programs does not currently permit the programs to be distributed by a 3rd party. BIRCH has scripts that completely automate the process of downloading, compiling, and installing all programs and documentation in the most recent version of FASTA.

These scripts download the FASTA programs using anonymous FTP.  To make it possible for the script to give your email address as the password (considered proper netiquette) you should have set the environment varible $MAILID to your email address. It's probably simplest to add the following line to
your .login file (if you use csh or ksh):

setenv MAILID user@host.domain.etc

or the following two lines to your .profile (bash, sh, ksh)

MAILID=user@host.domain.etc
export MAILID

Now, logout and login again and you can run the following scripts:

cd install-birch/fasta
./fasta2install.csh
./fasta3install.csh
That's all there is to it! These scripts automatically download the shar archives from ftp.virginia.edu/pub/fasta, run the appropriate makefile, set global read and execute permissions, and copy the programs into the appropriate directories.

Notes:
  1. Solaris cc compiler - Bill Pearson's Makefile.sun defaults to use the Sun cc compiler, which is often not available on many Solaris systems. Therefore, the fasta install scripts use gcc, and to do this the scripts will replace 'cc' in Makefie.sun with a call to gcc, using appropriate switches. BIRCH admins who wish to use the Sun cc compiler can run the install scripts using the -S option. eg. fasta2install.csh -S  or fasta3install.csh -S.
  2. These scripts expect that the environment variables $BIRCH, $BIRCH_PLATFORM and $BIRCH_BIN are set, which is why you needed to logout and log back in in the previous step.
  3. This will take awhile because of the time required for compilation. Go get lunch or something.
  4. Each script creates a working directory ie. fasta2 and fasta3. All files, including source code, object files, documentation etc. will remain after the script has been terminated. If something went wrong with the compilation, the original files are still available for manual compilation. Otherwise, these directories can be deleted after all programs are installed.
  5. The file $doc/fasta/FASTA_LIST gives instructions for getting onto a mailing list if you wish to be informed of new FASTA releases. Running these scripts at any time, without modification should automatically update to the current version.


Please send suggestions of comments regarding this page to psgendb@cc.umanitoba.ca