-
-
-## Examining Files
-
-We now know how to move around the file system and look at the
-contents of directories, and create files - but how do we look at the contents of files? Obviously we could open files up with a text editor like `nano` but there MUST be a better way!
-
-The easiest way to examine **a small file** (i.e. few enough lines, that we could easily scroll through) is to just print out all of the contents using the command `cat`. Print the contents of `spider.txt` by entering the following command:
-
-```bash
-$ cat spider.txt
-```
-
-This prints out the all the contents of `spider.txt` to the screen.
-
-> `cat` stands for catenate; it has many uses and printing the contents of a files onto the terminal is one of them.
-
-`spider.txt` is all of 3 lines. When you have a 100000 line file you hardly want to print the entire thing to screen (and it can take a while!). When you are working on the cluster for data analysis you will inevitably encounter with large files.
-
-For **large files** the command, `less`, can be useful. Let's take a look at the files in the `raw_fastq` folder. You can check the size of them by using the command `ls -lh`. This will give you the size of them in human readable format.
-
-```bash
-$ cd ~/unix_lesson/raw_fastq
-
-$ ls- lh
-```
-
-These files are quite large, so we probably do not want to use the `cat` command to look at them. Instead, we can use the `less` command. Let's try this with one of the files.
-
-```bash
-less Mov10_oe_1.subset.fq
-```
-
-We will explore FASTQ files in more detail later, but notice that FASTQ files have four lines of data associated with every sequence read. Not only is there a header line and the nucleotide sequence, similar to a FASTA file, but FASTQ files also contain quality information for each nucleotide in the sequence.
-
-The `less` command opens the file, and lets you navigate through it.
-Shortcuts for `less`
-
-| key | action |
-| ---------------- | ---------------------- |
-| SPACE | to go forward |
-| b | to go backwards |
-| g | to go to the beginning |
-| G | to go to the end |
-| q | to quit |
-
-`less` also gives you a way of searching through files. Just hit the / key to begin a search. Enter the name of the string of characters you would like to search for and hit enter. It will jump to the next location where that string is found. If you hit / then ENTER, `less` will just repeat the previous search. `less` searches from the current location and works its way forward. If you are at the end of the file and search for the word "cat", `less` will not find it. You need to go to the beginning of the file and search.
-
-For instance, let's search for the sequence `GAGACCC` in our file. You can see that we go right to that sequence and can see what it looks like. To exit hit q.
-
-There's another way that we can look at files, and in this case, just
-look at part of them. This can be particularly useful if we just want
-to see the beginning or end of the file, or see how it's formatted.
-
-The commands are `head` and `tail` and they just let you look at
-the beginning and end of a file respectively.
-
-```bash
-$ head Mov10_oe_1.subset.fq
-```
-
-
-```bash
-$ tail Mov10_oe_1.subset.fq
-```
-
-Now that we have shown you how to create files, edit them and examin them - let's move on to the next lesson to learn more!
-
-
-*This lesson has been developed by members of the teaching team at the [Harvard Chan Bioinformatics Core (HBC)](http://bioinformatics.sph.harvard.edu/). These are open access materials distributed under the terms of the [Creative Commons Attribution license](https://creativecommons.org/licenses/by/4.0/) (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.*
-
-* *The materials used in this lesson were derived from work that is Copyright © Data Carpentry (http://datacarpentry.org/).
-All Data Carpentry instructional material is made available under the [Creative Commons Attribution license](https://creativecommons.org/licenses/by/4.0/) (CC BY 4.0).*
-* *Adapted from the lesson by Tracy Teal. Original contributors: Paul Wilson, Milad Fatenejad, Sasha Wood and Radhika Khetani for Software Carpentry (http://software-carpentry.org/)*
diff --git a/new_basic_shell/04_shell_scripts.md b/new_basic_shell/04_shell_scripts.md
deleted file mode 100644
index 67a96761..00000000
--- a/new_basic_shell/04_shell_scripts.md
+++ /dev/null
@@ -1,154 +0,0 @@
----
-title: "Shell scripts"
-author: "Meeta Mistry, Bob Freeman, Mary Piper, Radhika Khetani, Jihe Liu, Will Gammerdinger, Emma Berdan"
----
-
-Approximate time: 20 minutes
-
-## Learning Objectives
-
-- Contrast shell scripts with direct commands
-
-
-## Shell scripts
-
-By this point in the module you have been introduced to a number of commands to explore your data. To demonstrate the function of each command we have run them one at a time at the command prompt. The command prompt is useful for testing out commands and also performing simple tasks like exploring and organizing the file system. When we are **running analyses which require a series of tasks to be run**, there is a more efficent way to do this using **shell scripts**.
-
-Shell scripts are **text files that contain commands we want to run**. Here we will introduce you to shell scripts by providing a simple example.
-
-
-### A simple script
-
-We are finally ready to see what makes the shell such a powerful programming environment. To create our first script, we are going to take some of the commands we have run previously and save them into a file so that we can **re-run all those operations** again later, by typing just **one single command**. For historical reasons, a bunch of commands saved in a file is referred to as shell script, but make no mistake, this is actually a small program!
-
-#### File extension for shell scripts
-Interestingly, when working with Shell or on the command line you can give files any (or no) extension (.txt, .tsv, .csv, etc.). Similarly, for a shell script you *don't need a specific extension*. However, it is **best practice to give shell scripts the extension `.sh`**. This is helpful to your future self and your collaborators to identify that a given file is a shell script.
-
-Move over to the `other` directory and create a new file using `vim`. We will call our script `listing.sh`:
-
-```bash
-$ cd ~/unix_lesson/other
-$ nano listing.sh
-```
-
-#### Adding commands to our script
-
-This shell script will do two things:
-
-1. Tell us our current working directory
-2. List the contents of the directory
-
-We already know the commands for doing both of these things so let's add the 2 commands into our script, with a comment for each:
-
-```bash
-# Print working directory
-pwd
-
-# List contents of the directory
-ls -l
-```
-
-Now, let's save and quit this shell script. This should bring you back to the command prompt. Check and see that the new script file you created is in this directory:
-
-```bash
-$ ls -l
-```
-
-#### Running our script
-
-The `bash` command is typically used to start a new Bash shell session. However, if you provide it an argument, it treats that argument as the name of a script file to be run. To run the shell script you can use the `bash` command, or a short form of it, the `sh` command, followed by the name of your script:
-
-```bash
-$ sh listing.sh
-```
-
-_Did it work as you expected? Do you see the output printed to your console?_
-
-### Best practices for shell scripts
-
-This is a very simple shell script, just to introduce you to the concept. Before we jump into more scripts which better demonstrate their utility, we will take a moment to cover a few adjustments we would make to our script which we consider best practice when writing shell scripts.
-
-#### Shebang!
-
-Open up the script with `nano`. At the beginning of our script we are going to add what is called a **shebang line**.
-
-```bash
- #!/bin/bash
-```
-
-This line is the **absolute path to the Bash interpreter**. The shebang line ensures that the bash shell interprets the script even if it is executed using a different shell.
-
-**Why do I need a shebang line? My scripts ran perfectly well before without it.**
-
-Having a shebang line is best practice. Your script runs fine without it, because in our current environment bash is the default shell. We mentioned previously that there are various flavors of the shell, and if your system defaults to something other than bash the script will not work. To avoid any issues, we explicitly state that this script needs to executed using the bash shell.
-
-#### Adding verbosity
-
-Our example script is quite short, and therefore is quick to run. In practice your scripts will be longer, and probably more computationall intensive. In these situations it would be great to have some report of what your script is doing as it works through the commands. This is also super useful when troubleshooting.
-
-An easy way to add verbosity is to **use the `echo` command**. The `echo` command is used to display a line of text that is passed in as an argument. This is a bash command that is mostly used in shell scripts to output status to the screen or to a file.
-
-We can include an `echo` statement for each command that we are running in our script:
-
-```bash
-#!/bin/bash
-
-echo "Your current working directory is:"
-pwd
-
-echo "These are the contents of this directory:"
-ls -l
-
-```
-
-Save your script and quit `nano`. Try running this script and see how our edits impact the output!
-
-_Were the `echo` commands helpful in letting you know what came next?_
-
-
-***
-
-**Exercise**
-
-1. Open up the script `listing.sh` using vim. Add the command which prints to screen the contents of the file `Mov10_rnaseq_metadata.txt`.
-2. Add an echo statement for the command, which tells the user "This is information about the files in our dataset:"
-3. Run the new script. Report the contents of the new script and the output you got after running it.
-
- Answer
--The itsy bitsy spider -Went up the water spout -Down came the rain --
-
-
-
-
-***
-
-*This lesson has been developed by members of the teaching team at the [Harvard Chan Bioinformatics Core (HBC)](http://bioinformatics.sph.harvard.edu/). These are open access materials distributed under the terms of the [Creative Commons Attribution license](https://creativecommons.org/licenses/by/4.0/) (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.*
-
-* *The materials used in this lesson were derived from work that is Copyright © Data Carpentry (http://datacarpentry.org/).
-All Data Carpentry instructional material is made available under the [Creative Commons Attribution license](https://creativecommons.org/licenses/by/4.0/) (CC BY 4.0).*
-* *Adapted from the lesson by Tracy Teal. Original contributors: Paul Wilson, Milad Fatenejad, Sasha Wood and Radhika Khetani for Software Carpentry (http://software-carpentry.org/)*
diff --git a/new_basic_shell/Lesson5_tocome.md b/new_basic_shell/Lesson5_tocome.md
deleted file mode 100644
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--- a/new_basic_shell/Lesson5_tocome.md
+++ /dev/null
@@ -1,11 +0,0 @@
-SO SO MUCH!
-
-Automate everything!
-
-Answers
-Question 1
- Add this command to listing.sh using vim:
- cat Mov10_rnaseq_metadata.txt
Question 2
- Add this command to listing.sh using vim:
- echo "This is information about the files in our dataset:"
Question 3
- sh listing.sh
Your current working directory is: - /home/mm573/unix_lesson/other - These are the contents of this directory: - total 240 - -rw-rw-r-- 1 mm573 mm573 346 Sep 30 12:47 directory_info.sh - -rw-rw-r-- 1 mm573 mm573 193 Oct 5 14:53 listing.sh - -rw-rw-r-- 1 mm573 mm573 93 Sep 30 10:40 Mov10_rnaseq_metadata.txt - -rw-r--r-- 1 mm573 mm573 1057 Sep 30 10:40 sequences.fa - -rw-rw-r-- 1 mm573 mm573 48 Oct 5 14:49 spider.txt - This is information about the files in our dataset: - sample celltype - OE.1 Mov10_oe - OE.2 Mov10_oe - OE.3 Mov10_oe - IR.1 normal - IR.2 normal - IR.3 normal-
-
-
Screw manual labor, learn to make the computer do everything!
*** diff --git a/new_basic_shell/README.md b/new_basic_shell/README.md deleted file mode 100644 index 3f8fe184..00000000 --- a/new_basic_shell/README.md +++ /dev/null @@ -1,64 +0,0 @@ -## Introduction to the Command Line Interface - -| Audience | Computational skills required | Duration | -:----------|:----------|:----------| -| Biologists | None | 2-3 hour workshop (~3 hours of trainer-led time)| - - -### Description - -This repository has teaching materials for a **2-3 hour**, hands-on **Introduction to the command-line interface** workshop led at a relaxed pace. - - -### Learning Objectives - -* Recognize the importance of bash in the analysis of high throughput sequencing (HTS) data -* Install and locate the software/tools necessary for accessing the command line -* Describe the organization of the file directory and how to move through it -* Demonstrate different ways to manipulate files, such as moving, copying, and renaming -* Compare different commands for examining small or large files -* Create new files and make edits to existing files with nano -* Contrast shell scripts with direct commands - - -> These materials are developed for a trainer-led workshop, but also amenable to self-guided learning. - - -### Contents - -| Lessons | Estimated Duration | -|:------------------------|:----------| -|[Why Bash?]() | 15 min | -|[Acessing the Shell](Lesson1_Acesssingtheshell.md) | 15 min | -|[Moving around and basics](Lesson2_basics.md) | 45 min | -|[Creating Files and Searching](Lesson3_creatingfiles.md) | 45 min | -|[Shell Scripts](Lesson4_shellscripts.md) | 20 min | -|[Preview of other modules](Lesson5_tocome.md) | 15 min | - - - -### Dataset -[Introduction to Shell: Dataset](https://www.dropbox.com/s/t3lkyz1pz021222/unix_lesson.tar.gz?dl=1) - -### Installation Requirements - -***Mac users:*** -No installation requirements. - -***Windows users:*** -[GitBash](https://git-scm.com/download/win) - - -### Resources - -* Shell cheatsheets: - * [http://fosswire.com/post/2007/08/unixlinux-command-cheat-sheet/](http://fosswire.com/post/2007/08/unixlinux-command-cheat-sheet/) - * [https://github.com/swcarpentry/boot-camps/blob/master/shell/shell_cheatsheet.md](https://github.com/swcarpentry/boot-camps/blob/master/shell/shell_cheatsheet.md) -* [Explain shell](http://explainshell.com) - a web site where you can see what the different components of a shell command are doing. -* Software Carpentry tutorial: [The Unix shell](https://swcarpentry.github.io/shell-novice/) -* [Introduction HOW-TO Bash](https://tldp.org/HOWTO/Bash-Prog-Intro-HOWTO.html) - ---- - -*These materials have been developed by members of the teaching team at the [Harvard Chan Bioinformatics Core (HBC)](http://bioinformatics.sph.harvard.edu/). These are open access materials distributed under the terms of the [Creative Commons Attribution license](https://creativecommons.org/licenses/by/4.0/) (CC BY 4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.* - diff --git a/new_basic_shell/img/Slide1.jpg b/new_basic_shell/img/Slide1.jpg deleted file mode 100644 index 424b5a82..00000000 Binary files a/new_basic_shell/img/Slide1.jpg and /dev/null differ diff --git a/new_basic_shell/img/nano.png b/new_basic_shell/img/nano.png deleted file mode 100644 index eb224a13..00000000 Binary files a/new_basic_shell/img/nano.png and /dev/null differ diff --git a/new_basic_shell/img/open_sores.png b/new_basic_shell/img/open_sores.png deleted file mode 100644 index b2b9b208..00000000 Binary files a/new_basic_shell/img/open_sores.png and /dev/null differ diff --git a/new_basic_shell/img/readme.md b/new_basic_shell/img/readme.md deleted file mode 100644 index 21b8ba89..00000000 --- a/new_basic_shell/img/readme.md +++ /dev/null @@ -1 +0,0 @@ -image files diff --git a/new_basic_shell/img/simpsons.gif b/new_basic_shell/img/simpsons.gif deleted file mode 100644 index 077c41d1..00000000 Binary files a/new_basic_shell/img/simpsons.gif and /dev/null differ