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These are good guides for learning something about shell scripting,
http://linuxcommand.org/
http://www.howtogeek.com/67469/

This is also good, but more extensive and focused on bash,
http://www.tldp.org/LDP/Bash-Beginners-Guide/html/

One of the nicest things about learning to use cygwin and the bash shell 
is that it will make linux much more accessible if you ever want to go 
that route.

Other than shell scripting, the concept of a package manager is the 
other main thing you will need to gt well in hand.

The cygwin installer functions more or less as a package manager. 
Windows generally doesn't require the user to be involved in managing 
the underlying tools, libraries, etc, that allow software to run. In 
most cases, you just install software and the engineer who created the 
software takes care of making sure it runs. In linux, there are often 
dependent components that need to be installed to get an application to 
run. A package manager helps to control that aspects of software 
management. When you install an application with a package manager, the 
manager will check to make sure that everything the application needs is 
present and install additional components if necessary.

Packages that appear in the cygwin installer are maintained by 
volunteers who add updates to applications and dependent components and 
keep everything working. Installations can be made outside the package 
manager, but then you have to configure the dependencies your self. If 
you choose something to install in the cyginw installer, you will often 
be shown a window listing additional components that are also going to 
be installed.

It would be a good idea to read up a bit on package managers, but that 
info may be a bit harder to find than info on something like bash.

LMHmedchem


Jonathan Martin wrote:
>
>
> FANTASTIC!
>
>
> On Tuesday, December 31, 2013 5:20 PM, Eliot Moss <moss AT cs DOT umass DOT edu> wrote:
> My suggestion would be to take a look at some of the
> many books that try to introduce Unix and bash to new
> users and see how they have approached a good / logical
> order of presentation.
>
> cygwin itself is perhaps more directed at experienced
> users -- or in any case, it is making no particular
> attempt to be easier for novices to use than Unix is,
> or to provide special support for Unix novices.  But
> that does not preclude someone (you) from making such
> a thing and perhaps getting it adopted into the distro
> (I don't control that!).
>
> Perhaps similar efforts have been made for linux,
> which might give a starting point?
>
> Regards -- EM
>
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