...
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:
- Familiarize yourself with the way course material will be presented.
- Log into lonestar5.
- Change your lonestar profile to the course specific format.
- Refresh understanding of basic linux commands with some course organization.
- Review use of the nano text editor program, and become familiar with several other text editor programs.
...
| Code Block | ||
|---|---|---|
| ||
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.
...
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.
...
If you still see something else, let the instructor know.
This concludes the the linux and lonestar refresher/introduction tutorial.
Genome Variant Analysis Course 2020 home.
...