WICC Workshop March 14 2015

WICC2015_Notes

Github repo for Shell
https://github.com/suryasaha/shell-novice
Github repo web page
http://suryasaha.github.io/shell-novice/


Clone the repo
git clone https://github.com/suryasaha/shell-novice.git
OR
wget ftp://ftp.solgenomics.net/bioinfo_class/other/2015/nelle.zip
unzip nelle.zip


File for Perl exercises
ftp://ftp.solgenomics.net/bioinfo_class/other/2014/perl_class_files.zip

LECTURE NOTES

Shell Commands
whoami - Tells you what user you are logged in as
ls - tells you what's in the current folder
ls -l - tells you what's in the current folder (with more information)
ls directory - tells you what's in the given folder
unzip file.zip - Unzips a file
command1 | less - Shows you the output of command1 one page at a time.
touch filename - Creates the blank file filename
echo "text" > filename - Creates the file filename with the content text
cat - Displays the contents of a file
nano - A text editor.
nano filename - Edit the file with nano.
cd - Change the directory.
../ - The parent directory of the current directory.
mv oldpath newpath - Moving/renaming a file
wc - Count words/lines/characters in a file
wc -c - Count characters
wc -l - Count lines
sort - Sort its input by the first "column"
pico - Another text editor
wget - Download a file

Piping
command1 | command2
Takes the output of command1 and gives it as the input to command2.

Wildcard
Used in place of filenames.
* - All files in the current directory (e.g. wc -l *)

Organization of a UNIX System
/ - The "root" directory (like C:\ on Windows)

Perl
- An interpreted language

Hashes:
- Like Python's dictionary

Strict mode:
use strict;
use warnings;

Makes Perl be more strict about interpreting your code.
 
 Testing
 
 Static analysis tools
 - Catches bugs that the compiler cannot catch
 - C++ CppCheck, clang-analyze
 
 Dynamic analysis tools
 - Often slow but can catch bugs compiler and static analysis can miss
 - Many good tools ( valgrind for c/c++, 
 - Sanitizers (AddressSanitizer, ThreadSanitizer)
 
 Linters/Formatters for consistent formatting and layout
 - Perl (Perl Tidy, Perl Critic)
 - C(clang-format, clang-tidy)
 
 Documentation generators
 - JavaDoc, DoxyGen
 
 Your own tests
 - Google's include-what-you-need
 
 Property tests
 - Sample space of test inputs is generated based upon property