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Replace tutorial command with git clone #7

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9 changes: 5 additions & 4 deletions README.md
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Expand Up @@ -9,15 +9,15 @@ This tutorial focuses on a subset of the [Data Carpentry Genomics workshop curri

## Get Tutorial Files

Logged into the submit node, we will run the tutorial command, that will
Logged into the submit node, we will download the tutorial materials. This will
create a folder for our analysis, as well as some sample files.

```
tutorial bwa
git clone https://github.com/OSGConnect/tutorial-bwa
```

## Install and Prepare BWA
First, we need to install BWA, also called Burrows-Wheeler Aligner. To do this, we will create and navigate to a new folder in our /home directory called `software`. We will then follow the developer's instructions (https://github.com/lh3/bwa) for using `git clone` to clone the software and then build the tool using `make`.
First, we need to install BWA, also called Burrows-Wheeler Aligner. To do this, we will create and navigate to a new folder in our `/home` directory called `software`. We will then follow the developer's instructions (https://github.com/lh3/bwa) for using `git clone` to clone the software and then build the tool using `make`.

```
cd ~/tutorial-bwa
Expand Down Expand Up @@ -56,7 +56,7 @@ cd ~/tutorial-bwa/software
tar -czvf bwa.tar.gz bwa
```

Checking the size of this compressed tarball using `ls -lh bwa.tar.gz` reveals the file is approximately 4MB. The tarball should stay in /home.
Checking the size of this compressed tarball using `ls -lh bwa.tar.gz` reveals the file is approximately 4MB. The tarball should stay in `/home`.


## Download Data to Analyze
Expand All @@ -80,6 +80,7 @@ ls -lh data/trimmed_fastq_small
```

Once everything is downloaded, make sure you're still in the `tutorial-bwa` directory.

```
cd ~/tutorial-bwa
```
Expand Down