...
I expect the which command gives 1 line of data listing '/corral-repl/utexas/BioITeam/breseq/bin/breseq' and the 2nd command gives 'breseq 0.35.1', if so you do not have to clone your own copy of breseq, but it is still encouraged particularly if you envision using breseq in your own work outside of this course.
| Warning |
|---|
| title | Warning against an idev node |
|---|
|
Unlike most warnings you get about idev nodes during this class, this one is actually a warning against being on an idev node as idev sessions typically download files slower. |
Upgrading bowtie2
| Code Block |
|---|
| language | bash |
|---|
| title | download version 2.3.5.1 of bowtie2 to your src folder in work directory |
|---|
|
mkdir $WORK/src
cd $WORK/src
wget https://github.com/BenLangmead/bowtie2/releases/download/v2.3.5.1/bowtie2-2.3.5.1-linux-x86_64.zip
unzip bowtie2-2.3.5.1-linux-x86_64.zip |
...
| Info |
|---|
| title | Testing what happens if you load the bowtie/2.3.4 module |
|---|
|
As mentioned in an earlier tutorial, when you load a module TACC assumes you are about to use it and therefore appends the directories associated with the module at the front of the $PATH. Consider the output to the following block of code to figure out how you could rerun the mapping tutorial with bowtie2 version 2.3.4. | Code Block |
|---|
| language | bash |
|---|
| title | bowtie2 checks |
|---|
| which -a bowtie2
module load bowtie/2.3.4
which -a bowtie2
module unload bowtie/2.3.4
which -a bowtie2 |
Remember, when you use the -a option on a which command and have multiple lines of output, it is always the top line that is executed. |
Cloning breseq
As mention above, this is not required to complete other breseq based tutorials in the course, however, it is highly recommended for anyone who anticipates using breseq in their own work. Initially, cloning a github repository as exceptionally similar to using the wget command to download bowtie2 above, it involves typing 'git clone' followed by a web address where the repository is stored. As we did for installing bowtie2 with wget we'll clone the repository into a 'src' directory inside of $WORK.
| Code Block |
|---|
| language | bash |
|---|
| title | Using the mkdir command to create a folder named 'src' inside of your $WORK directory |
|---|
| collapse | true |
|---|
|
mkdir $WORK/src #If you already have a src directory, you'll get a very benign error message stating that the folder already exists and thus can not be created
cd $WORK/src |
In a web browser navigate to github and search for 'breseq' in the top right corner of the page. The top result will be for barricklab/breseq; click the green box for 'clone or download' and either control/command + C on the address listed, or click the clipboard icon to copy the repository address. This image may be helpful if you are are having trouble locating the green box.
| Code Block |
|---|
| language | bash |
|---|
| title | Once you have copied the address and are in the $WORK/src directory clone the repository with 'git clone' |
|---|
| collapse | true |
|---|
|
git clone https://github.com/barricklab/breseq.git |
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. Alternatively, you may get an error message saying "fatal: destination path 'breseq' already exists and is not an empty directory." This means you have previously clone the repository, don't worry that just means when you use the 'git pull' command in the compiling breseq section you will get a message saying a bunch of changes are being made rather than a message of 'already up to date' that a fresh cloning will show.
If you don't see said directory, or can't cd into that directory let the instructor know.
| Info |
|---|
| title | You may be thinking that this really does seem remarkably similar to the wget downloading you did for bowtie2 and wondering why you just don't do that |
|---|
|
The answer is that in the future if you want to upgrade to the latest version of breseq, rather than having to navigate to the github page, check if the version is different, copy the download link, you can now use the 'git pull' command to check if there is a new version available and automatically download it. Further git control allows you to more quickly roll back to an older version if you need to (say you want to add another small set of samples to an existing analysis that you did a year ago without wanting to have to rerun all the old samples). |
Compiling breseq
Much like how downloading bowtie2 was not enough to make it usable, the same will be true of breseq. Unlike bowtie2, rather than just editing our path or moving executable files around we have to compile the code.
| Code Block |
|---|
| language | bash |
|---|
| title | Command to compile the most recent version of breseq |
|---|
|
mkdir -p $HOME/local/bin
module unload bowtie/2.3.4
cd $WORK/src/breseq
git pull
make clean
./bootstrap.sh
./configure --prefix=$HOME/local
make
make install |
The above will take several minutes to complete, but should always be printing something something new to the screen within 30 seconds or less.
Testing breseq
| Code Block |
|---|
| language | bash |
|---|
| title | It is always a good idea to test the compilation after you use the make install command. |
|---|
|
make test |
This command is expected to take a total of ~13 minutes with no one step should take more than 30-60 seconds. Unfortunately, with all the the text scrolling around on the screen, it makes it difficult to notice that there are actually a number of different tests being conducted each of which can pass or fail as a way of informing you what exactly is going wrong. Just before you get a final report of how long the command took, you see a block of text that reads:
| No Format |
|---|
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO
Passed check
OOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOOO |
It is a good idea to
Next steps
Now that you have