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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.
Asking for tutorial or learning material recommendations is off-topic. I've mentioned below how you can run your Java program. – Karan – 2015-05-26T20:09:47.193
Could you elaborate on "can't seem to get anything to work"? Which specific problems/errors do you encounter? On a sidenote: While cygwin is excellent for unix-like behavior in some aspects, it is not a replacement, and as such can not fully provide some linux-fundamentals that some programs rely on. – Jarmund – 2015-05-26T20:48:42.697