Where do I put commands to run scripts?

debugcn Published at Dev

Gaius Augustus

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>

$ 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.

Karan

You need to install the Java Runtime Environment (JRE) to run JARs (which are compiled programs, not scripts).

The JAR can then be launched via the normal cmd command prompt (no Cygwin required) or even by double-clicking in Windows Explorer. Since you want to pass arguments to it you should run it from the command prompt.

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edited at2021-07-4

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