Stacks for Debian, packaged for Bio-Linux by Tim Booth
======================================================

The stacks command-line commands are all available as advertised, but you have
to type "stacks" as the first command - eg. instead of

  $ process_radtags -p ./raw/ -o ./samples/ -b ./barcodes/barcodes_lane3

run

  $ stacks process_radtags -p ./raw/ -o ./samples/ -b ./barcodes/barcodes_lane3

If you don't like this, just add /usr/lib/stacks/bin to your $PATH.

The Stacks web interface is available in the stacks-web package and will be added
to Apache so that it appears under http://localhost/stacks.

In the manual, the authors of Stacks have assumed that you are always running
Stacks on a personal worsktation, while DEB packages always have to assume
that they are being installed on a shared machine where users have restricted
priviliges.  On such a machine you would never run this:

  $ mysql
  mysql> GRANT ALL ON *.* TO 'stacks_user'@'localhost' IDENTIFIED BY 'stackspassword';

Because it opens up the whole of MySQL to anyone who knows this password (ie. everyone
who can log into the machine).

To deal with this, I've added a single convenience script which can be run under
sudo to make new databases and assign write perms to a user or users.  After this
the user can load data into the database and view it right away with no further
configuration or intervention by the sysadmin.

 $ sudo stacks-setup-database expt1
