From 023e35f8e11b05def0d17ce4d159f6b8a41bcc98 Mon Sep 17 00:00:00 2001 From: Chris Fields Date: Thu, 7 Jul 2016 15:14:02 -0500 Subject: [PATCH] markdownize file, minimal changes (looks fairly up to date) --- INSTALL-WIN.md | 87 +++++++++++++++++++++++++++------------------------------- 1 file changed, 40 insertions(+), 47 deletions(-) diff --git a/INSTALL-WIN.md b/INSTALL-WIN.md index bfed373f6..ebaabba2f 100644 --- a/INSTALL-WIN.md +++ b/INSTALL-WIN.md @@ -1,25 +1,16 @@ - - Installing Bioperl on Windows +# Installing BioPerl on Windows - Contents - - * 1 Introduction - * 2 Perl Options - * 3 Installing Perl on Windows - * 4 CPAN for Strawberry Perl and ActivePerl - * 5 Bioperl in Cygwin - -1 Introduction +# Introduction This installation guide was written by Barry Moore, Nathan Haigh -and other Bioperl authors based on the original work of Paul Boutros. The +and other BioPerl authors based on the original work of Paul Boutros. The guide has been updated by Paul Cantalupo and Francisco Ossandon. *Note* For Windows it is recommended to install BioPerl version 1.6.924 or newer, since many Windows-specific bugs from previous versions were fixed. Please report problems and/or fixes to the BioPerl mailing list. -2 Perl Options +# Perl Options There are a couple of ways of installing Perl on a Windows machine. One is to get the most recent build from [Strawberry Perl](http://strawberryperl.com/) @@ -41,7 +32,7 @@ see [ActivePerl MinGW PPM webpage](http://www.activestate.com/activeperl/downloa *Note* Support for installation through ActivePerl Perl Package Manager has been dropped in favor of CPAN. -3 Installing Perl on Windows +# Installing Perl on Windows 1. Download the [Strawberry Perl MSI](http://strawberryperl.com/releases.html) or [ActivePerl MSI](http://www.activestate.com/activeperl/downloads). 2. Run the Installer (accepting all defaults is fine). @@ -52,7 +43,7 @@ This approach is not recommended unless you have specific reasons for doing so and know what you're doing. [Cygwin](http://en.wikipedia.org/wiki/Cygwin) is a [UNIX](http://en.wikipedia.org/wiki/UNIX) -emulation environment for Windows and comes with its own copy of Perl. Information on Cygwin and Bioperl is found below. +emulation environment for Windows and comes with its own copy of Perl. Information on Cygwin and BioPerl is found below. ### Installation using the ActiveState Perl Package Manager @@ -61,10 +52,10 @@ BioPerl package produced for it was the old version 1.6.1 (2009) and many Windows-specific bugs were fixed in more recent versions 1.6.923 and 1.6.924. Please install using the CPAN instructions below. -4 CPAN for Strawberry Perl and ActivePerl +# CPAN for Strawberry Perl and ActivePerl Both CPAN and manual methods ultimately need the accessory compiling program -MinGW, which incorporates the necessary tools like dmake and gcc. MinGW comes +MinGW, which incorporates the necessary tools like `dmake` and `gcc`. MinGW comes by default with Strawberry Perl, but must it be installed through PPM for ActivePerl (CPAN will display a warning if not present). Also, CPAN need to be upgraded to >= v1.81, [Module::Build](https://metacpan.org/pod/Module::Build) @@ -84,29 +75,29 @@ the release for newest version 5.22 it's still not available (December 2015). ### Start the install with CPAN -1) Open a cmd window by going to `Start >> Run` and typing `cmd` +1. Open a cmd window by going to `Start >> Run` and typing `cmd` into the box and pressing return. -2) Type `cpan` to enter the CPAN shell. +2. Type `cpan` to enter the CPAN shell. -3) At the `cpan>` prompt, type `install CPAN` to upgrade to the +3. At the `cpan>` prompt, type `install CPAN` to upgrade to the latest version. -4) Quit (by typing 'q') and reload CPAN. You may be asked some +4. Quit (by typing 'q') and reload CPAN. You may be asked some configuration questions; accepting defaults is fine. -5) At the `cpan>` prompt, type `o conf prefer_installer MB` to tell +5. At the `cpan>` prompt, type `o conf prefer_installer MB` to tell CPAN to prefer to use `Build.PL` scripts for installation, and the type `o conf commit` to save that choice. -6) At the `cpan>` prompt, type `install Module::Build`. +6. At the `cpan>` prompt, type `install Module::Build`. -7) At the `cpan>` prompt, type `install Test::Harness`. +7. At the `cpan>` prompt, type `install Test::Harness`. -8) At the `cpan>` prompt, type `install Test::Most`. +8. At the `cpan>` prompt, type `install Test::Most`. ### Finish the install with CPAN -You can now follow the instructions INSTALLING BIOPERL THE EASY WAY +You can now follow the instructions INSTALLING BioPerl THE EASY WAY USING CPAN in the INSTALL file. ### Finish the install with BioPerl from GitHub @@ -114,50 +105,52 @@ USING CPAN in the INSTALL file. For the bleeding edge version install manually using a ZIP file from the GitHub repository: -1) Go to [GitHub](https://github.com/bioperl/bioperl-live) and press the +1. Go to [GitHub](https://github.com/BioPerl/BioPerl-live) and press the `Download ZIP` button. -2) Extract the archive in the normal way. +2. Extract the archive in the normal way. -3) In a cmd window `cd` to the directory you extracted to. Eg. if -you extracted to directory 'bioperl-live', `cd bioperl-live` +3. In a cmd window `cd` to the directory you extracted to. Eg. if +you extracted to directory 'BioPerl-live', `cd BioPerl-live` -4) Type `perl Build.PL` and answer the questions appropriately. +4. Type `perl Build.PL` and answer the questions appropriately. -5) Type `perl Build test`. All the tests should pass, but if they don't, -[let us know](https://github.com/bioperl/bioperl-live/issues). Your usage of -Bioperl may not be affected by the failure, so you can choose to continue +5. Type `perl Build test`. All the tests should pass, but if they don't, +[let us know](https://github.com/BioPerl/BioPerl-live/issues). Your usage of +BioPerl may not be affected by the failure, so you can choose to continue anyway. -6) Type `perl Build install` to install Bioperl. +6. Type `perl Build install` to install BioPerl. -5 Bioperl in Cygwin +# BioPerl in Cygwin Cygwin is a Unix emulator and shell environment available free at -http://www.cygwin.com. Some users claim that installation of Bioperl is +http://www.cygwin.com. Some users claim that installation of BioPerl is easier within Cygwin than within Windows, but these may be users with UNIX backgrounds. A note on Cygwin: it doesn't write to your Registry, it doesn't alter your system or your existing files in any way, it doesn't create -partitions, it simply creates a *cygwin/* directory and writes all of its +partitions, it simply creates a `cygwin/` directory and writes all of its files to that directory. To uninstall Cygwin just delete that directory. -To get Bioperl running first install the basic Cygwin package as well as +To get BioPerl running first install the basic Cygwin package as well as the Cygwin `perl`, `make`, `binutils`, and `gcc` packages. Clicking the View button in the upper right of the installer window enables you to see details on the various packages. Then start up Cygwin and follow the -Bioperl installation instructions for UNIX in Bioperl's INSTALL file. +BioPerl installation instructions for UNIX in BioPerl's `INSTALL` file. -Cygwin paths +## Cygwin paths If you're trying to use some application or resource outside of the Cygwin directory and you're having a problem remember that Cygwin's path syntax -may not be the correct one. Cygwin understands */home/jacky* or -*/cygdrive/e/cygwin/home/jacky* (when referring to the E: drive) but the -external resource may want *E:/cygwin/home/jacky*. So your *rc files may end +may not be the correct one. Cygwin understands `/home/jacky` or +`/cygdrive/e/cygwin/home/jacky` (when referring to the E: drive) but the +external resource may want `E:/cygwin/home/jacky`. So your `*rc` files may end up with paths written in these different syntaxes, depending. -For example, here's how to set the environmental variable TMPDIR, programs +For example, here's how to set the environmental variable TMPDIR, programs like BLAST and clustalw need a place to create temporary files: - setenv TMPDIR e:/cygwin/tmp # csh, tcsh - export TMPDIR=e:/cygwin/tmp # sh, bash +``` +setenv TMPDIR e:/cygwin/tmp # csh, tcsh +export TMPDIR=e:/cygwin/tmp # sh, bash +``` -- 2.11.4.GIT