#######################################
            General Bash
######################################

top
	- system monitor

ps -ef | grep perl
	- shows all processes running that match with perl
	- the f shows the command that was used to start the process

kill <pid>
	- ends a pid in the process list (-ps)
	- use kill -9 <pid> for a stronger kill

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ls -a 
   - shows all files, including hidden

ls -l 
	- shows permissions of files in directory
	- shows bytes of each file too
	- add h (ls -lh) for display mb
	- pipe to more to wait to print (ls -lh | more)

------------------------------------------

du -hs <directory name>
	- gets the size of the directory in GB

df -h <directory name>
	- gets the percentage of disk space used in the directory
	- also shows amount used and amount remaining
	- df -h /home/ for percentage used on total machine

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chmod ugo+wrx <directory name or filename>
	- gives all permissions


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sudo apt-get install <packageName>
   - downloads and installs a linux package

sudo apt-cache search <keyword>
   - searches for a linux package name

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emacs .bashrc
   - edits the .bashrc file
   - should be called when in home directory (e.g. /home/<username>)

source .bashrc
	- allows you to use your newly modified .bashrc file (call after editing it)


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tail -f <filename>
	- displays the end of a file as it grows
	- useful for monitoring nohup.h as it runs

less <filename>
	- like more but allows scrolling.  ctrl + d to get to the end

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rm -rf <dir>
	- remove a directory and all files/subfolders in it

rm *~
	-removes all files with a tilda in current directory


#########################################
            Perl and CPAN
########################################

sudo perl -MCPAN -e shell
   > install <ModuleName>::<Package Name>
   > m <Module Name>


#######################################
        Git on SourceForge
#######################################

initial commit:
	git init
	git config user.name <username>
	git config user.email <username>@users.sourceforge.net
	git remote add origin ssh://<username>@git.code.sf.net/p/<directory>
	git add --all
	git commit -a -m 'Initial commit'
	git push -u origin master

subsequent commits:
	git add --all
	git commit -a -m '<commit comment>'
	git push -u origin master


clone a code to a new machine:
	git clone ssh://<username>@git.code.sf.net/p/<directory>
	git config user.name <username>
	git config user.email <username>@users.sourceforge.net

merge local code from remote code:
	git pull origin master

replace local code with remote code:
	git fetch origin
	git reset --hard origin/master


#############################################
                Jasmine
############################################

FTP:
	sftp -oPort=20025 <username>@jasmine.cs.vcu.edu
	   -connects to jasmine with ftp
	get <filename>
	   - downloads from ftp to local directory
	put <filename>
	   - uploads from local to ftp

SSH:
	ssh -p 20025 -Y <username>@jasmine.cs.vcu.edu
	   - ssh for jasmine, then enter password at prompt

	nohup <command> >& <STDOUT file> &
	   - allows processes to run in the background and without a terminal being open
	   - good for submitting jobs
	   - all stdout is output to the <STDOUT file> (optional)