Thank you for including me in your discussions on Debian distribution of bioinformatics programs.
I have been distributing Bioinformatics programs for almost 30 years (I distributed some programs back in the mid-70's on punch cards), and the FASTA program (and its predecessor, FASTP) has been distributed for about 20 years. It has mostly been my experience that the difficulties that biologists have using FASTA, or programs like them, would be reduced very slightly by providing a binary distribution. It is very easy to compile FASTA - the only libraries required are the standard 'C' library, and the math library. So different architectures, and different versions of Linux, really don't pose a problem. It can be difficult to install FASTA in a way that makes it easy for users to find the sequence databases. Not only do the databases need to be downloaded, but users must understand something about the different sequence flat file formats, and, for things to be really easy, a configuration file must be edited to list the names and locations of the sequence databases. Most people who have problems with FASTA have problems at this step. But FASTA sometimes has bugs (which are usually rather subtle), at which point it is helpful for users to contact me. Genuine bugs are of great concern to me; I try to fix them within a week. My experience with FASTA WWW sites is that users sometimes find a problem, but do not tell me about it. I like people to get the program from me, so they can contact me about it. Often, the first thing I will do is suggest that they download a current version of the program. That's a sensible suggestion if they got the program from me originally, but can be quite confusing if it came as part of a Linux distribution (does updating their Linux distribution update FASTA?). Thus, I believe that scripts that download the current version of FASTA, and databases (databases are available from ftp.ebi.ac.uk/ and ftp.ncbi.nih.gov/) are more useful for most Bioinformatics users than FASTA binaries. Bill Pearson -- To UNSUBSCRIBE, email to [EMAIL PROTECTED] with a subject of "unsubscribe". Trouble? Contact [EMAIL PROTECTED]
