I'm trying to run a few scripts (whether python, java, etc). The developers in their documentation give code for me to put in. Here are some examples:

```
java -Xmx2g -jar muTect-XXXX-XX-XX.jar
--analysis_type MuTect
--reference_sequence <reference>
--cosmic <cosmic.vcf>
--dbsnp <dbsnp.vcf>
--intervals <intervals_to_process>
--input_file:normal <normal.bam>
--input_file:tumor <tumor.bam>
--out <call_stats.out>
--coverage_file <coverage.wig.txt> 

```

or

```
$ sudo easy_install virtualenv

```

Here's what I've done so far:
1) In windows 7, I've installed Cygwin; 2) I've installed Ubuntu for any Linux based computing.

My problem: I've tried putting these into cygwin, changing all the references to my file paths and the like. However, I can't seem to get anything to work. I assume I'm doing something very basic wrong. Does anyone have any insight or a VERY BASIC tutorial on how to get started? I'm not even sure what search terms to use in Google to find this kind of thing.

Thanks for any help.