README for bioweb.tar.gz 

- a Bioinformatics web interface to molecular biology software,
including GCG and EMBOSS packages, phylogenetics and related
bioinformatics tools.

The bioweb2-sol.tar.gz archive file is that used on our local
system, with a few binaries for Solaris, though mostly this is
Perl code and configuration files.

This is primarily the Pise interface (Perl based, web anonymous
access), and W2H (Perl, secure web to user accounts).  Indiana
Univ. Center for Genomics and Bioinformatics is in the process of
putting these parts together with free and commercial (for local
use) bioinformatics tools, and will make the freely distributable
parts available here, as the bioweb.tar files.

Currently this set needs documentation for installation and
addition of packages. You are likely better off with the Pise and
W2H package installers.  However, you should be able to unpack
this set on a Sun Solaris system, and hook into an Apache-like
web server.  We will be adding documentation for installation and
use.

The default installation path used is
  /bio/local/web
with molecular biology applications in the folder
  /bio/local/mb

/bio/local/web has

bin/      conf/     lib/      pise/     w2h/
cgi-bin/  htdocs/   logs/     server@   w2huser/

The configuraton in conf/ directory is used for
inclusion  in web server configurations (http and https).
The bin/ has a few binary executables needed by Pise and
symbolic links for applications.  The htdocs contains
the primary web interface and documentation.  Lib includes
Perl library files.  w2h/ provides the https secure user account
access to GCG and EMBOSS software. It needs to be configured
following directions for the w2h package for a given site.

/bio/local/mb has binaries for the programs, our local
collection includes these, with separate location for GCG
software:

ae2/               fasta/             paml/              scan_for_matches/
bin/               fasta1/            phrap/             seqpup/
birch/             fastdnaml/         phylip/            seqpup06/
blast/             gde@               phylip34/          staden/
blast2@            gde22/             predator/          tkdcse_home/
chem-flex/         homochart/         primer/            tree-puzzle/
clustalw1.7/       initenv            prosite/           treealn/
clustalw1.8/       mapmaker/          rasmol/            treetool/
coresearch/        mase/              readseq/           worm/
dnarates/          misc/              restrict-map/
emboss/            nentrez/           rna/


-- Don Gilbert and Sue Olson, Indiana U. CGB
-- June 2002