Improve the documentation of Smith-Waterman + bundle sample data

[cogumbreiro]

It would be nice to bundle some sample data with the Smith-Waterman example. As it stands run_test.sh is breaking (see error message below).

It seems to me that the README is mentioning xstack and CnC-OCR unnecessarily, as it works perfectly fine with iCnC for example.

Finally, it would be nice to mention the tuning parameters again and possibly cross-reference the tuning section of the wiki.

Recommendations

• bundle some sample input
• fix run_test.sh to use said sample input
• update README so as to avoid mentioning XSTG_ROOT or OCR as the exemple is not specific to these platforms
• list the tuning parameters and cross-reference the wiki section on tuning

Error log of run_test.sh

 $ ./run_test.sh 
make: Nothing to be done for 'install'.
Testing string1-small.txt vs string2-small.txt with width=3, height=3
cd ./install/icnc && \
 ./SmithWaterman 3 3 /home/tiago/Work/cnc-framework/examples/SmithWaterman/xstg/apps/apps/smithwaterman/datasets/string1-small.txt /home/tiago/Work/cnc-framework/examples/SmithWaterman/xstg/apps/apps/smithwaterman/datasets/string2-small.txt
Tile width:  3
Tile height: 3
Could not open file: /home/tiago/Work/cnc-framework/examples/SmithWaterman/xstg/apps/apps/smithwaterman/datasets/string1-small.txt
Makefile:123: recipe for target 'run' failed
make: *** [run] Error 1
FAIL
Testing string1-large.txt vs string2-large.txt with width=569, height=661
cd ./install/icnc && \
 ./SmithWaterman 569 661 /home/tiago/Work/cnc-framework/examples/SmithWaterman/xstg/apps/apps/smithwaterman/datasets/string1-large.txt /home/tiago/Work/cnc-framework/examples/SmithWaterman/xstg/apps/apps/smithwaterman/datasets/string2-large.txt
Tile width:  569
Tile height: 661
Could not open file: /home/tiago/Work/cnc-framework/examples/SmithWaterman/xstg/apps/apps/smithwaterman/datasets/string1-large.txt
Makefile:123: recipe for target 'run' failed
make: *** [run] Error 1
FAIL

[cogumbreiro]

@DaoWen, I am happy to work on this issue if you are happy with it. Unfortunately I am not knowledgeable on the details of tuning --- as in, I can't explain what each tuning file is doing --- so I would need your help on improving that part of the documentation (see #14).

[DaoWen]

@cogumbreiro: It would be great if you can make any of the improvements here or in #14. Pull requests are welcome on the code in this repo. As for the wiki, unfortunately I don't think GitHub lets you do PRs for wiki updates, so this might be a good process to follow instead:

1. git clone https://github.com/habanero-rice/cnc-framework.wiki.git
2. Push the wiki repo into a public git repo on your account
3. Make your changes on a branch
4. Open a pull request from your branch to the master branch
5. @mention me in your PR so I get a notification, and I'll review the changes for accuracy
6. I'll use the .patch file generated by your PR to apply your changes to the actual wiki

[cogumbreiro]

Cool. I will work on this issue then.
Regarding #14 I will definitely need more input from your side.