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a web-service devoted to the detection and analysis of VNTR loci (Variable Number of
Tandem Repeats).  If you have another tool making use of Polloc, [please let us
know](mailto:lrr@cpan.org?subject=Polloc%20tool).

### How can I contribute to the Polloc project?

The Polloc library is Open Source, and is licensed under the Perl Artistic License.  This
means that you can freely modify the code provided you properly cite the source.  However,
if you want your modifications to be incorporated into the main Polloc code, please fork
[Polloc at GitHub](http://www.github.com/lmrodriguezr/Polloc) and submit your changes via
Pull Requests.  If you are not familiar with Git, please read the documentation available
at the [git website](http://www.git-scm.com/).

### Where can I find the documented modules in human-readable format?

You can read the documentation of Polloc in HTML format at CPAN:
(http://search.cpan.org/dist/Polloc/).

### The tests failed, should I force installation?

It is very hard to predict the behavior your are going to experience with Polloc if you
install it with failed tests.  Instead, we prepared a generic troubleshooting for failed
tests we have observed either at the CPAN tester matrix or running installations in our
machines:

#### Test `t/05-typing/02-typing.t` failure 1

Are you reading a message like this?:

```
t/05-typing/02-typing.t ............ 1/13 Use of uninitialized value in concatenation (.) or string at /Library/Perl/5.10.0/Bio/Tools/Run/Alignment/Muscle.pm line 427.
sh: - : invalid option
Usage:	sh [GNU long option] [option] ...
	sh [GNU long option] [option] script-file ...
GNU long options:
	--debug
	--debugger
	--dump-po-strings
	--dump-strings
	--help
	--init-file
	--login
	--noediting
	--noprofile
	--norc
	--posix
	--protected
	--rcfile
	--restricted
	--verbose
	--version
	--wordexp
Shell options:
	-irsD or -c command or -O shopt_option		(invocation only)
	-abefhkmnptuvxBCHP or -o option

--------------------- WARNING ---------------------
MSG: Muscle call crashed: 512 [command  -in /tmp/_YS2FojZj7  -out /tmp/7BP7tE2dKG/fwsAmEh1NG 2> /dev/null]

---------------------------------------------------
Can't call method "average_percentage_identity" on an undefined value at /Users/luismrodriguezr/.cpan/build/Bio::Polloc-1.0503-xA5_RC/blib/lib/Bio/Polloc/LociGroup.pm line 376.
# Looks like you planned 13 tests but ran 6.
# Looks like your test exited with 2 just after 6.
t/05-typing/02-typing.t ............ Dubious, test returned 2 (wstat 512, 0x200)
Failed 7/13 subtests 
```

This very verbose message often means one thing: you have `Bio::Tools::Run::Alignment::Muscle` installed in
your system, but you don't have Muscle.  The solution is pretty easy: install muscle, available at
[Robert Edgar's website](http://www.drive5.com/muscle/downloads.htm).

#### Test `t/05-typing/02-typing.t` failure 2

Or, instead, are you reading a message like this?:

```
t/05-typing/02-typing.t ............ 1/13 sh: primersearch: command not found
t/05-typing/02-typing.t ............ 7/13 
#   Failed test 'The thing isa ARRAY'
#   at t/05-typing/02-typing.t line 35.
#     The thing isn't defined

#   Failed test at t/05-typing/02-typing.t line 36.
#          got: '-1'
#     expected: '0'

#   Failed test at t/05-typing/02-typing.t line 37.
#          got: undef
#     expected: '105'

#   Failed test at t/05-typing/02-typing.t line 42.
#          got: undef
#     expected: '1'
# Looks like you failed 4 tests of 13.
t/05-typing/02-typing.t ............ Dubious, test returned 4 (wstat 1024, 0x400)
Failed 4/13 subtests 
```

This is far less verbose, but again means you lack required software in your machine.  This time, it is
the `primersearch` utility of EMBOSS.  The solution: install EMBOSS, available at
[Sourceforge](http://emboss.sourceforge.net/download/).

#### Other errors?

If you have non-listed failures, please do not hesitate to
[contact us](mailto:lrr@cpan.org?subject=Polloc%20Unknown%20failure), or directly register them at
[GitHub](http://www.github.com/lmrodriguezr/Polloc/issues).