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swvanderlaan authored Sep 27, 2017
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Expand Up @@ -2,27 +2,7 @@ GWASToolKit
============
This repository contains various scripts in Perl, BASH, and Python scripts to use in genome-wide association studies, single variant analyses, regional analyses, and gene-centered analyses using data of the Athero-Express Genomics Studies 1 and 2 (AEGS), AAA-Express Genomics Study (AAAGS), or CTMM Genomics Study (CTMM).

Scripts will work within the context of a certain Linux environment (in this case a CentOS7 system on a SUN Grid Engine background).

All scripts are annotated for debugging purposes - and future reference.

The installation procedure is quite straightforward, and only entails two steps consisting of command one-liners that are *easy* to read. You can copy/paste each example command, per block of code. For some steps you need administrator privileges. Follow the steps in consecutive order.

```
these `mono-type font` illustrate commands illustrate terminal commands. You can copy & paste these.
```

To make it easier to copy and paste, long commands that stretch over multiple lines are structered as follows:

```
Multiline commands end with a dash \
indent 4 spaces, and continue on the next line. \
Copy & paste these whole blocks of code.
```

Although we made it easy to just select, copy and paste and run these blocks of code, it is not a good practise to blindly copy and paste commands. Try to be aware about what you are doing. And never, never run `sudo` commands without a good reason to do so.

We have tested GWASToolKit on CentOS6.6, CentOS7, and OS X El Capitan (version 10.11.[x]).
All scripts are annotated for debugging purposes - and future reference. The scripts will work within the context of a certain Linux environment (in this case a CentOS7 system on a SUN Grid Engine background). As such we have tested GWASToolKit on CentOS6.6, CentOS7, and OS X El Capitan (version 10.11.[x]).


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