/usr/share/doc/stacks/README.Debian is in stacks 2.0Beta8c+dfsg-1.
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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
privileges. 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
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