a message for commit, I talked about bashrc

commandline.md

@@ -1,15 +1,95 @@
+http://www.emoji-cheat-sheet.com/
+
 # Command line cheatsheet
 
 This is a cheat sheet for "Bourne-again shell" (bash) and GNU/Linux commands.
+## The basics:
+```
+	cd ~ 					go to home directory
+	clear					clear terminal
+	source					reload this file
+	mkdir					make directory
+	rm -rf					Remove recursively and force
+	chmod ###				777 is the most generous, order:  user, group, everyone
+	more					Contents shows up below printed to terminal
+	less					bring up the document, but remove it from the screen and terminal on Q
+	cat					can view (print to terminal) can also pipe data to other things, concatenate vertically
+	>					Output to a file (can replace the file if it already exists) Called "redirecting"
+	>> 					append to existing file (does not replace existing file, only appends)
+	mv					Cut and Paste (copy but remove source)
+	cp					copy (retain source)
+	tree -f					prints out a directory structure tree (stop doing cd ls recursively!) -f option prints full paths on every branch
+	du -ch					display disk use (-c sum all subfolders) (-h make human readable)
+	ln -s					soft links	Source Destination
+	which 					find the path to the object specified
+	ls -lhaH				human-readable sizes, permissions, groups, and symbolic links displaying fullpaths
+	qstat -r hotel | less			Show all jobs on the group “hotel”
+	qstat -u ucsd-train03			show job status list for the user “ucsd-train03”
+	qsub script.sh				submit script (which has PBS flags) to the queue
+	tee					Write to something and submit it to a program (see manual)
+	who					On TSCC this lists all of the logged in users and their IP addresses
+	pwd -P					Print physical directory "what drive am I on?"
+	top				What jobs are running?
+	screen				See: https://kb.iu.edu/d/acuy
+	git ls-files			Which files are managed by git
+	git ls-files -u			Which files are unmerged or have conflicts
+	git log				show all commits that have happened with these files (use to find commit hash if you want to reset)
+	git reset (hash)		reset to certain commit (find hash with git log)
+	git checkout --ours		use everything that is yours when you merge
+	git checkout --theirs		use everything that is theirs when you merge
+
+	Mac-Only: 
+	hdiutil attach /path	Mount a disk image via command line
+	hdiutil info			Tell me about mounted disk images
+	hdiutil detach /dev/disk1s2	detach image at specified location if you don't know it, use the info command^
+
+```
+## How basic program inputs and outputs work:
+Standard in
+to
+#####Program
+outputs two outputs
+###### 1) Standard out (stdout)
+###### 2) Standard Error (stderr)
+
+You can redirect either or both E.G. ```grep NFKB tfs.bed 1>tfs.nfkb.bed 2>tfs.nfkb.err```
+
+If you don't specify the stream that you want it will just redirect the standard out and alternatively print the standard error output to the command line (E.G. grep:tfs.bed: No such file or directory).
+
+###Advanced:
+On TSCC if you write  
+2>&1
+as the last line, you will cat your standard error and out files to standard out
+
+#TSCC
+when you are in your home directory on the login node, you are writing to the login node, the login node has very little available ram per user (5 login nodes * 64GB /#Users)
+
+when you are in your scratch directory, you are writing to the scratch directory
+
+when you submit to qsub, you are assigned a host machine based on your request (#PBS scripts) for processors, memory, etc. AT THE MOMENT YOU MAKE THE REQUEST. If other tasks go out of control and start taking up more memory it can fuck things up quickly for everyone on that host.
+
+If you disconnect from the login node while writing to Scratch, it cuts off whatever you are currently writing and leaves a corrupted file.  USING THE HEAD NODE IS RISKY. If they want to install an update and bring down your login node, you're boned. If you've submitted your stuff as a job you are far more protected.
+
+To load pre-installed software on TSCC (biotools, etc https://www.sdsc.edu/support/user_guides/tscc-quick-start.html#applications) use the command:
+'''
+module load biotools
+'''
 
-## Text maninpulation
 
-### Skip the first line of a file
+## Text maninpulation
+### Navgiation 
+```
+Control + E 		Jump to end of the line
+Control + A		Jump to start of the line
+Alt + ErrorKeys		Jump between words on the same line
+```
+## Skip the first line of a file
 
 ```
 tail -n +2 filename.txt
 ```
 
+
 ## Compressing and decompressing files
 
 ### Create a gzipped tarball from a `*` glob command
@@ -92,3 +172,72 @@ To install a program from source on a shared cluster, you will often need to spe
 ./configure --prefix=/projects/ps-yeolab/software
 make && make install   # "make install" will run only if "make" is successful
 ```
+
+### Screens
+Always use the same login node!
+```
+screen -S try1
+```
+[detached]
+
+```
+screen -S try2
+```
+[detached]
+
+```
+screen -x
+```
+There are several suitable screens on:
+	40357.try1	(Detached)
+	40451.try2	(Detached)
+
+Type 
+```
+screen [-d] -r [pid.]tty.host" 
+```
+to resume one of them.
+```
+screen -x 40357.try
+```
+[screen is terminating]
+
+```
+screen -x
+```
+[screen is terminating]
+
+
+### .bashrc
+
+#####This is where you put all of the stuff you want to execute, load, echo, etc when you login to TSCC!
+```
+nano ~/.bashrc
+```
+
+##### On your local machine:
+```
+nano ~/.bash_preferences
+```
+##### For using "screens"
+```
+nano ~/.screenrc
+```
+
+### Installing biotools
+```
+mothership:~ mbaughn$ pip install biotools
+Collecting biotools
+  Downloading biotools-1.2.12.tar.gz
+Building wheels for collected packages: biotools
+  Running setup.py bdist_wheel for biotools ... done
+  Stored in directory: /Users/mbaughn/Library/Caches/pip/wheels/86/0e/ec/57f244b7a14c7847b55636f1900206b5039b38828372cafd87
+Successfully built biotools
+Installing collected packages: biotools
+Successfully installed biotools-1.2.12
+```
+
+##### Windows Firewall -- Block an Individual IP Address:
+```
+netsh advfirewall firewall add rule name="Intuit1" dir=out interface=any action=block remoteip=75.98.51.173
+```