Setting Up JBrowse on Windows via Cygwin

• ash

• binutils

• diffutils

• expat

• gcc

• make

• nano

• ncftp

• pcre

• perl

• rcs

• rebase

• unzip

• wget

Once Cygwin is intalled you'll need to configure the HOME Environment variable.

• "Set the HOME environment variable to c:\cygwin\home\YOURUSER, where YOURUSER is your userid, e.g. jsmith or administrator.
  • Windows NT, XP and 2000: Go into Control Panel, double-click the System icon, and select Advanced, then click Environment Variables. Under User Variables, click New.... Now type HOME (must be upper case) as the variable name, and c:\cygwin\home\YOURUSER as the value, and hit OK." --Instructions taken from http://biowiki.org/view/TWiki/WindowsInstallCookbook#Cygwin_Unix_tools_Perl_and_RCS

Now start up cygwin and enter the following commands ($ indicates the command prompt) $ mount -b -c /cygdrive

From here you can follow the use the bioperl installation for unix instructions found here: http://www.bioperl.org/wiki/Installing_Bioperl_for_Unix#BIOPERL_INSTALLATION. You'll find the same basic info below but I'll go through what exactly I did. Open cygwin and enter the following commands:

> perl -MCPAN -e shell
cpan>install Bundle::CPAN
cpan>q

If you get a .dll error during this process you need to rebase your .dlls. To do this exit cygwin but open up the root cygwin folder in windows explorer. Open the bin directory and double click on ash.exe. This will open an instance of the ash shell. Here execute the command: "rebaseall -v". This should clear up the .dll problem. You can reenter the previous commands and CPAN will continue where it left off. Once that's finished proceed with the following commands

>cpan
cpan>install Module::Build
cpan>o conf prefer_installer MB
cpan>o conf commit
cpan>q

Now download the bioperl package here: http://bioperl.org/DIST/ You should use the most recent version, I downloaded "BioPerl-1.6.0.tar.gz" If you can't extract the tarball install 7zip or download the .zip version. Extract the archive in your cygwin home directory.

Start up cygwin and cd to this new directory. Then enter the following commands

>perl Build.PL
>./Build install

Now that Bioperl is installed we need JSON. Get it here: http://search.cpan.org/CPAN/authors/id/M/MA/MAKAMAKA/JSON-2.16.tar.gz Extract the tarball into the cygwin home directory. cd into the JSON directory. Enter the following commands:

>perl Makefile.PL
>make
>make test
>make install

Now grab JBrowse here: http://github.com/jbrowse/jbrowse Extract it into the cygwin home directory and you're ready to get started with JBrowse on Windows.

If you get errors saying there is a problem with @INC, then the Bioperl path has not been added to the Perl path library. You can correct this by specifying a new enviroment variable,"PERLLIB" with value equal to the path of your Bioperl files. If you get permission errors specify a new enviroment variable called "CYGWIN" with value "nontsec".