You can add

export JULIA_PKGDIR=C:/Users/you/.julia

to then end of your .bashrc file in Cygwin.

For git, check the order of things in
run(`which -a git`)

from inside Julia. If the git that's part of Julia comes before Cygwin's 
/usr/bin/git, I think you should be okay.

On Saturday, September 17, 2016 at 6:30:31 AM UTC-7, zlqs1985 wrote:
> Hi,tony, thanks for timely and insightful reply. Unfortunately, I'm new to 
> cygwin (linux) and not quite sure what step should I take to make the the 
> job done. For example, where can I find the julia package path, and to 
> which I add these path in cygwin, with which command ("export" as I 
> guess?). For the git issue, I think I first need to uninstall the git 
> package in cygwin and then call git outside, is that true? Thank you for 
> your help.
> 在 2016年9月17日星期六 UTC+8下午8:33:11,Tony Kelman写道:
>> When you run a login terminal in Julia, your HOME is set differently than 
>> outside of Cygwin. You could set the environment variable JULIA_PKGDIR to 
>> your normal package directory. Note that if you're using Julia 0.4, you 
>> should avoid having Cygwin's git in your path, or have it later than the 
>> version of git that comes with Julia 0.4. The Julia package manager isn't 
>> compatible with Cygwin's version of git, but on Julia 0.5 the package 
>> manager no longer uses command-line git so it's not an issue.
>> On Saturday, September 17, 2016 at 2:15:57 AM UTC-7, zlqs1985 wrote:
>>> I want to make Cygwin  my default julia working env. It proved that I 
>>> can dive into julia successfully within cygwin. However, when I want to use 
>>> package ,say 
>>> using Distributions
>>> , the cmd throwed error message told me that : ArgumentError: 
>>> distribution not found in path
>>> Well, it's clear I have not added the package path to cygwin, an action 
>>> I take for granted in windows cmd.
>>> Can  linux command like 
>>> export PATH=/cgdrive/c/ .. julia package path .. :$PATH
>>> resolve my problem? Any suggestion are highly appreciated.

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