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This is probably the longest tutorial in the entire class. It is designed to take between 1/2 and 3/4 of the first class. Do not stress if you feel people are moving through it faster than you are, or if you do not get it done before the next presentation. There will be links back to this tutorial from other tutorials as needed, and by the 2nd half of Wednesday's class when we start with the specialized tutorials, you can circle back to this tutorial as well. 

Objectives:

1. Familiarize yourself with the way course material will be presented.
2. Log into lonestar5.
3. Change your lonestar profile to the course specific format.
4. Refresh understanding of basic linux commands with some course organization.
5. Review use of the nano text editor program, and become familiar with several other text editor programs.

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There will be 4 types of code blocks used throughout this class. Text inside of code blocks represent "right" answersat least 1 possible correct answer, and should either be typed EXACTLY into the terminal window as they are, or copy pasted with . There is a notable exception . Text that exist within text between <> symbols represent something that you need to replace before sending it to the terminal. Yes, the <> marks themselves also need to be replaced. We try to put informative text within the brackets so you know what to replace it with. If you are ever unsure of what to replace the <> text with, just ask.

1. Visible
   1. These are code blocks that you would have no idea what to type without help. (like when a new command is being introduced)
   2. These will typically be associated with longer/more detailed text above the text box explaining things.

   3. An example code block showing you the command you need to type into the prompt to list what directory you are currently in:

      Code Block
      language bash
      pwd

2. Hinted
   
   1. These are code blocks that you can probably figure out what to type with a hint that goes beyond what the tutorial is requesting. Access the hint by clicking the triangle or hint hyperlink text.
   2. These exist to force you to think about what command you need, and hopefully make some connections to help you remember what you will need to type in the future.
   3. These should all come with additional explanation as to what is going on.
   4. Rather than just expanding these by reflex, I strongly suggest seeing if you can figure out what the command will be, and checking your work

   5. Example:

      Expand
      title what command would you use to Print your current Working Directory
      In this example the letters P W and D are all capitalized to try to help you focus on the command itself Code Block language bash pwd

3. Hidden:
   1. These code blocks represent things that you should have seen several times already, or things that can be succinctly explained.

   2. Example:

      Code Block
      language bash title use the pwd command to print your current working directory collapse true
      pwd

4. Speed bump:

   1. This combines the previous 2 types to deliberately slow you down and be cumbersome. 
   2. If you find yourself consistently wrong about what eventually shows up in the text box, slow down, step back, think about whats going on, and consider asking a question.
   3. These should only come after you have seen the same (or very similar) commands in the other formats previously

   4. Example:

      Expand
      title print your current working directory
      Remember, the command you need is "pwd". Code Block language bash title This command needs no options collapse true pwd

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ls              #ignore everything that comes after the # mark. There is a problem on this wiki page but things after a # wont effect commands

ls -a

ls -a -1

ls -a -l

ls -a -1

ls -al

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exitlogout
# or
logoutexit

then log back in:

ssh <username>@ls5.tacc.utexas.edu

If everything is working correctly you should now see a this as your prompt like this:  

tacc:~$

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cdh
ln -s $SCRATCH scratch
ln -s $WORK work
ln -s $BI BioITeam

Several people report seeing an error message stating "ln: failed to create symbolic link 'BioITeam/BioITeam': Permission denied." This is being investigated, but is not expected to impact today's tutorial.

• Understanding what your .bashrc file actually does.

cat .bashrc

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• Linux text editors installed at TACC (nano, vi, emacs). These run in your terminal window. vi and emacs are extremely powerful but also quite complex, so nano may be  is the best choice as a first local text editor. Text editors If you are already familiar with one of the other programs you are welcome to continue using it.
• Text editors or IDEs that run on your local computer but have an SFTP (secure FTP) interface that lets you connect to a remote computer (Notepad++ or Komodo Edit). Once you connect to the remote host, you can navigate its directory structure and edit files. When you open a file, its contents are brought over the network into the text editor's edit window, then saved back when you save the file.
• Software that will allow you to mount your home directory on TACC as if it were a normal disk e.g. MacFuse/MacFusion for Mac, or ExpanDrive for Windows or Mac ($$, but free trial). Then, you can use any text editor to open files and copy them to your computer with the usual drag-drop.

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1. The most important thing to get used to is the convention of using . or _ in  _  or capitalizing the first letter in each word in names rather than spaces in names, and limiting your use of any other punctuation. Spaces are great for mac and windows folder names when you are using visual interfaces, but on the command line, a space is a signal to start doing something different. Imagine instead of a BioITeam folder you wanted to make it a little easier to read and wanted to call it "Bio I Team" certainly everyone would agree its easier to read that way, but because of the spaces, bash will think you want to create 3 folders, 1 named Bio another named I and a third named Team. Now this is certainly behavior you can use when appropriate to your advantage, but generally speaking spaces will not be your friend. Early on in my computational learning I was told "A computer will always do exactly what you told it to do. The trick is telling it to do what you want it to do". 
2. Name things something that makes it obvious to you what the contents are not just today but next week, next month, and next year even if you don't touch the it for weeks-months-years.

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When you execute the ls -1 > whatisHere command, you should have noticed nothing happening happened on the screen, and when you cat the whatisHere file, you should notice the output you would have expected from the ls -1 > whatisHere command. Often it is useful to chain commands together using the output of the first command as the input of the second command. Commands are chained together using the "|" character (shift \ above the return key). Use redirection to put the first 2 lines of the $BI directory contents into the whatisHere file.

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mv whatisHere BioIteam_contents
mv whatisHere BioIteam_directory_contents
mv whatisHere BioIteam_directory_contents_2020-06

• Understanding TACC

Now that we've been using lonestar for a little bit, and have it behaving in a way that is a little more useful to us, let's get more of a functional understanding of what exactly it is and how it works.

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 cp $WORK/my_fastq_data/*fastq $SCRATCH/my_project/

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1. Job: Not required by the script, but likely always will be. This file has a list of commands that you want to run, and is probably biggest part of what makes tacc great... letting you run a large number of commands all at once rather than having to run them 1 at a time on your own computer.
   
2. Time and name: They are required so obviously important for that reason. Also names are important as mentioned above naming everything 'tacc_job' will make your life much more confusing at some point.
3. Wayness: 12 is the default, 48 is the max on lonestar. 
   1. This is a balance of memory and to a lesser extent speed against how long you want to wait for your job to run and SU cost. 
   2. Imagine you have 96 commands you want to run. 12, 24, and 48 as the "w" option will require 8, 4, and 2 remote computers to run at the same time, 2 computers are typically available sooner than a set of 4 and 4 are available sooner than a set of 8. So your job is likely to spend less time 'in the queue' with larger numbers.
   3. We'll go over "SUs" near the end of the course, but for now it is sufficient to say they are a currency for tacc, and that smaller numbers will cost more SUs
   4. For bacterial work, 48 is a much better choice in nearly all situations, unless you are experiencing problems or know you have a massive amount of data.
   5. The downside is if you pick a number that is too small, your commands may have errors and not actually produce results requiring you to start over with longer requests, or smaller "w" values
4. queue: Development and normal are the 2 you are likely to deal with most often. normal "Normal" is a better choice unless you are developing new code .or have odd turn around time requirements.

Running a job

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# remember that things after the # sign are ignored by bash 
# lines in code blocks like this often will scroll to the right if you have a narrow browser window
cds  # move to your scratch directory
mkdir my_first_job  # make a new folder called "my_first_job"
cd my_first_job  # move into the new folder to make it easier to create a file there
nano commands  

cat commands > commands.out  # this will print the contents of the file you are currently editing to a new file called commands.out
date > date.out  # this will create a file with todays date on it
pwd > current_directory.out  # this will create a file with the current directory in it
echo "my name is <YOURNAME>" >> name.out  # Note that this time we used the append symbol >> not the write symbol > as we plan to put multiple things into the same file. Be sure to replace the <> signs with your name
echo "This is the final result of my first script. It worked how I thought it would, or hopefully have the resources to figure out why it didn't" >> name.out  # this will add another line of text to the name.out file.
# feel free to add up to 7 more lines to your commands file here using the cat/ls/pwd/mkdir/other commands that you know.
# beware using cd commands here as it will change your directory as if you were doing it on an interactive node and may cause you to reference files that don't exist interactive node and may cause you to reference files that don't exist

# write and exit nano now ctrl-o ctrl-x
launcher_creator.py -n "my_first_job" -j commands -t 00:02:00 -a "UT-2015-05-18" # this will create a my_first_job.slurm file that will run for 2 minutes
sbatch my_first_job.slurm  # this will actually submit the job to the Queue Manager and if everything has gone right, it will be added to the development queue.

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You will notice when you type module list you have several different modules installed already. These come from both TACC defaults (TACC, linux, etc), and several that are used so commonly both in this class and by biologists that it becomes cumbersome to type "module load python2python3" all the time and therefore we just have them turned on by default by putting them in our profile to load on startup.  As you advance in your own data analysis you may start to find yourself constantly loading modules as well. When you become tiered of doing this (or see jobs fail to run because the modules that load on the compute nodes are based on your .bashrc file plus commands given to each node), you may want to add additional modules to your .bashrc file. This can be done using the "nano .bashrc" command from your home directory.

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unzip Trimmomatic-0.39.zip
cd Trimmomatic-0.39
cp trimmomatic-0.39.jar $HOME/local/bin

If you don't see the zip file or are unable to cd into the 0.39 directory after unzipping it let the instructor know.

As this tutorial is focused only on downloading interesting programs you may read about, this is the final step. If you do the optional trimmomatic tutorial later in the course, we'll go over some of the nuances of trimmomatic and shortcuts to make it easier to use. This page will be updated to include a link to said tutorial later in the week.

wget alternative

It is always an alternative to download such files directly to your computer using a web browser and then use the scp command to transfer it to TACC. The wget command can help you avoid these intermediate steps and is more convenient most of the time unless you want to install the program on both your laptop and TACC, and have the same operating system on both.

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You will see several download indicators increase to 100%, and when you get your command prompt back the ls command will show a new folder named 'breseq' containing a set of files. If you don't see said directory, or can't cd into that directory let the instructor know.

As with Trimmomatic, these files will require additional work that is somewhat specific to the specific program and there for beyond the scope of this tutorial. A link to the advanced tutorials for getting your own copy of breseq up and running will be added later in the week. 

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This is about using the pip3 install command. pip is the standard package manager for the common programing language python. When labs put together new analysis programs/packages, increasingly they try to make these programs available for others to use via pip. pip3 rather than just pip references the current specific version of python.

Here we will install the multiqc analysis program which compiles reports from a program called fastqc about the quality of fastq files from multiple different samples at one time. In the later portion of the class you may choose to work with this program to get a better overall view of multiple fastq files all at once rather than clicking through individual reports.

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If you still see something else, let the instructor know.

The multiqc tutorial can be found here.

This concludes the the linux and lonestar refresher/introduction tutorial.

Genome Variant Analysis Course 2020 home.

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