# Module

Multiple versions of various software packages are available on luria.mit.edu Versions are managed using [module](http://modules.sourceforge.net/).

**module commands**

* List available applications on the system:

```
module avail
```

* Load an application so it can be used:

```
module add
```

* Specify version number of an application, e.g.

```
module add tophat/2.0.12
```

We recommend you always module add the version number so that you know which version of the software is used. Otherwise, a running application may generate different results or break when the software is upgraded in the future.

Note: some packages are available only after you load the python (for python packages) or jre (for java packages) modules. For example, compare the output of the following:

```
module avail
```

with

```
module add jre/1.6.0-29
module add python/2.7.2
module avail
```

* R and R packages - Various versions of R are installed on luria. Each one has a collection of associated packages. Execute the following commands taking note of the comment lines:

```
# Load an R version
module add r/2.15.3
# Start R
R
```

* Once inside R, check out the available R packages

```
#List R packages and direct the list into an object called "a"
a<-installed.packages()
#Display the dimensions of the object "a"
dim(a)
#List the parts of object "a" that have package name and package version
a[,c(1,3)]
```

* **NOTE:** Those package version numbers may not be consistent from month to month and can change without warning.
* When working with R, capture your session info with the command below so you can reproduce the environment if needed:

```
sessionInfo()
```

* quit R

```
q(save="yes")
#enter y at prompt
```

* Once back in the shell, view the R data that remains

```
ls -lat | head
cat .Rhistory
```

* List loaded applications:

```
module list
```

* Unload an application:

```
module del
```

* Print module help:

```
module help
```