+docs

README.md

@@ -16,10 +16,9 @@ is much much more!
 
 Features
 ========
-* Executes scripts easily, no programming or even terminal use experience
-  needed.
-* Reports the exact command executed, so you can reproduce, automate, and report
-  analyses easily.
+* Executes scripts easily, no programming experience necessary.
+* Reports the exact command executed so you can easily log, reproduce, automate,
+  and report analyses.
 * Detached execution, so you can run multiple analyses at the same time.
 * Self-updating, so you always get the latest version of our scripts.
 * Zero configuration, just download and open.
@@ -40,10 +39,48 @@ two genomes:
 And the result window:
 ![aai result](docs/img/aai-result.png)
 
+Install
+=======
+Prerequisites
+-------------
+You'll only need a [Java Virtual Machine][10] to open the GUI. However, you
+might need other Software installed in your computer to execute certain scripts.
+Notably, you'll need [Perl][11] to execute any of the tasks ending in `.pl` and
+[Ruby][12] to execute any of the tasks ending in `.rb`. Also, the few tasks
+ending in `.bash` will require a GNU Bash port in Windows machines, and some
+tasks have additional requirements that are unlikely to ever work in Windows.
+That said, we're trying to extend our support as wide as possible, so please
+[report any issues][13]. Finally, some tasks might depend on external software
+like [BLAST][14].
+
+Linux or BSD
+------------
+1. Download `enveomics.jar`.
+2. Make sure you have [Java][10] or another implementation like [OpenJDK][15],
+   and use it to open `enveomics.jar`. In most modern Linux distros you can
+   simply right-click on the file and select to open with JVM or OpenJDK, or
+   even just double-click the file. If it doesn't work please [let us know][13],
+   and execute this in the terminal: `java -jar enveomics.jar`, changing the
+   path of `enveomics.jar` to wherever you downloaded it.
+
+Mac OS X
+--------
+We're currently working on packaging an OS X app, but in the meantime you can:
+1. Download `enveomics.jar`
+2. Execute this in the terminal: `java -jar -XstartOnFirstThread enveomics.jar`,
+   changing the path of `enveomics.jar` to wherever you downloaded it.
+
+Windows
+-------
+Our current pre-release is yet to be tested in Windows. If you're not affraid of
+finding bugs, just follow the same instructions above for Linux or BSD. And
+whatever happens, please [let us know][13].
+
 Coming soon
 ===========
 * Support for `enveomics.R`.
 * Input multiple files for scripts supporting them.
+* Easy installation, so terminal use is eliminated.
 
 Credits
 =======
@@ -66,3 +103,9 @@ Enveomics GUI and the [Enveomics collection][1] are licensed under the terms of
 [7]: http://enveomics.blogspot.com/2013/09/fastqsplitpl.html
 [8]: https://github.com/shoes/shoes4 "Shoes 4"
 [9]: https://thenounproject.com/yuluck
+[10]: https://www.java.com/en/download/
+[11]: https://www.perl.org/get.html
+[12]: https://www.ruby-lang.org/en/documentation/installation/
+[13]: https://github.com/lmrodriguezr/enveomics-gui/issues
+[14]: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download
+[15]: http://openjdk.java.net/

TODO.md

@@ -11,6 +11,7 @@ To Do
   rest-client gem in aai.rb/ani.rb.
 * Check for available updates (instead of relying on user checking).
   Perhaps with the github API?
+* Auto-add :requires based on the language (ruby, perl, bash, etc).
 
 History
 =======