Installing Bioperl on Windows

From DrugPedia: A Wikipedia for Drug discovery

Contents 1 Introduction 2 Requirements 3 Installation using the Perl Package Manager 3.1 GUI Installation 3.2 Comand-line Installation 4 Installation using CPAN or manual installation 5 Bioperl 6 Perl on Windows 7 Bioperl on Windows 8 Beyond the Core 8.1 Setting environment variables 8.2 Installing bioperl-db 9 Bioperl in Cygwin 10 bioperl-db in Cygwin 11 Cygwin tips 12 MySQL and DBD::mysql 13 Expat 14 Directory for temporary files 15 BLAST 16 Compiling C code

[edit] Introduction

This installation guide was written by Barry Moore, Nathan Haigh and other Bioperl authors based on the original work of Paul Boutros. The guide was updated for the BioPerl wiki by Chris Fields and Nathan Haigh.

Please report problems and/or fixes to the BioPerl mailing list.

[edit] Requirements

Only ActivePerl >= 5.8.8.819 is supported by the Bioperl team. Earlier versions may work, but we do not support them. ActivePerl 5.10 also works; however Template:PM parsing is broken in perl 5.10 (this has been fixed and will be made available in an upcoming release).

One of the reason for this requirement is that ActivePerl >= 5.8.8.819 now use Perl Package Manager 4 (PPM4). PPM4 is now superior to earlier versions and also includes a Graphical User Interface (GUI). In short, it's easier for us to produce and maintain a package for installation via PPM and also easier for you to do the install! Proceed with earlier versions at your own risk.

To install ActivePerl:

1) Download the ActivePerl MSI from ActiveState

2) Run the ActivePerl Installer (accepting all defaults is fine).

[edit] Installation using the Perl Package Manager

[edit] GUI Installation

1) Start the Perl Package Manager GUI from the Start menu.

2) Go to Edit >> Preferences and click the Repositories tab. Add a new repository for each of the following (note the difference based on the perl version):

Repositories to add

Name	perl 5.8	perl 5.10
BioPerl-Regular Releases	http://bioperl.org/DIST	http://bioperl.org/DIST
Kobes	http://theoryx5.uwinnipeg.ca/ppms	http://cpan.uwinnipeg.ca/PPMPackages/10xx/
Bribes	http://www.Bribes.org/perl/ppm	http://www.Bribes.org/perl/ppm

3) Select View >> All Packages.

4) In the search box type bioperl.

5) Right click the latest version of Bioperl available and choose install. (Note for users of previous Bioperl releases: you should not have to use the Bundle-BioPerl package anymore.)

5a) From bioperl 1.5.2 onward, all 'optional' pre-requisites will be marked for installation. If you see that some of them complain about needing a command-line installation (eg. XML::SAX::ExpatXS), and you want those particular pre-requisites, stop now (skip step 6) and see the 'Command-line Installation' section.

6) Click the green arrow (Run marked actions) to complete the installation.

[edit] Comand-line Installation

1) Follow steps 1) and 2) from 'GUI Installation' above, if you haven't done so already.

2) Open a cmd window by going to Start >> Run and typing 'cmd' and pressing return.

3) Type the following into the cmd window:

ppm-shell
search bioperl
install #

(where the number matches the bioperl version needed) You can use '-force' to force install if needed.

[edit] Installation using CPAN or manual installation

Installation using PPM is preferred since it is easier, but if you run into problems, or a PPM isn't available for the version/package of BioPerl you want, or you want to choose which optional dependencies to install, you can install manually by downloading the appropriate package or by using CPAN. In fact both methods ultimately need nmake to be installed, CPAN to be upgraded to >= v1.81, Template:CPAN to be installed (>= v0.2805) and Template:CPAN to be upgraded to >= v2.62:

1) Download nmake

2) Double-click to run it, which extracts 3 files. Move both NMAKE.EXE and the NMAKE.ERR files to a place in your PATH; if set up properly, you can move these to your Perl bin directory, normally C:\Perl\bin.

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.

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 configuration questions; accepting defaults is fine.

5) At the cpan> prompt, type 'o conf prefer_installer MB' to tell CPAN to prefer to use Build.PL scripts for installation. Type 'o conf commit' to save that choice.

6) At the cpan> prompt, type 'install Module::Build'.

7) At the cpan> prompt, type 'install Test::Harness'.

You can now follow the unix instructions for installing using CPAN, or install manually:

8) Download the .zip version of the package you want.

9) Extract the archive in the normal way.

10) In a cmd window 'cd' to the directory you extracted to. Eg. if you extracted to directory 'Temp', 'cd Temp\bioperl-1.5.2_100'

11) Type 'perl Build.PL' and answer the questions appropriately.

12) Type 'perl Build test'. All the tests should pass, but if they don't let us know. Your usage of BioPerl may not be affected by the failure, so you can choose to continue anyway.

13) Type 'perl Build install' to install BioPerl.

[edit] Bioperl

Bioperl is a large collection of Perl modules (extensions to the Perl language) that aid in the task of writing Perl code to deal with sequence data in a myriad of ways. Bioperl provides objects for various types of sequence data and their associated features and annotations. It provides interfaces for analysis of these sequences with a wide variety of external programs (BLAST, FASTA, clustalw and EMBOSS to name just a few). It provides interfaces to various types of databases both remote (GenBank, EMBL etc) and local (MySQL, Flat_databases flat files, GFF etc.) for storage and retrieval of sequences. And finally with its associated documentation and mailing lists, Bioperl represents a community of bioinformatics professionals working in Perl who are committed to supporting both development of Bioperl and the new users who are drawn to the project.

While most bioinformatics and computational biology applications are developed in UNIX/Linux environments, more and more programs are being ported to other operating systems like Windows, and many users (often biologists with little background in programming) are looking for ways to automate bioinformatics analyses in the Windows environment.

Perl and Bioperl can be installed natively on Windows NT/2000/XP. Most of the functionality of Bioperl is available with this type of install. Much of the heavy lifting in bioinformatics is done by programs originally developed in lower level languages like C and Pascal (e.g. BLAST, clustalw, Staden etc). Bioperl simply acts as a wrapper for running and parsing output from these external programs.

Some of those programs (BLAST for example) are ported to Windows. These can be installed and work quite happily with Bioperl in the native Windows environment. Some external programs such as Staden and the EMBOSS suite of programs can only be installed on Windows by using Cygwin and its gcc C compiler (see Bioperl in Cygwin, below). Recent attempts to port EMBOSS to Windows, however, have been mostly successful:

• EMBOSS ftp site
• EMBOSS 2.10

If you have a fairly simple project in mind, want to start using Bioperl quickly, only have access to a computer running Windows, and/or don't mind bumping up against some limitations then Bioperl on Windows may be a good place for you to start. For example, downloading a bunch of sequences from GenBank and sorting out the ones that have a particular annotation or feature works great. Running a bunch of your sequences against remote or local BLAST, parsing the output and storing it in a MySQL database would be fine also.

Be aware that most Bioperl developers are working in some type of a UNIX environment (Linux, OS X, Cygwin). If you have problems with Bioperl that are specific to the Windows environment, you may be blazing new ground and your pleas for help on the Bioperl mailing list may get few responses (you can but try!) - simply because no one knows the answer to your Windows specific problem. If this is or becomes a problem for you then you are better off working in some type of UNIX-like environment. One solution to this problem that will keep you working on a Windows machine it to install Cygwin, a UNIX emulation environment for Windows. A number of Bioperl users are using this approach successfully and it is discussed in more detail below.

[edit] Perl on Windows

There are a couple of ways of installing Perl on a Windows machine. The most common and easiest is to get the most recent build from ActiveState, a software company that provides free builds of Perl for Windows users. The current (October 2006) build is ActivePerl 5.8.8.819. Bioperl also works on Perl 5.6.x but due to installation problems etc, only ActivePerl 5.8.8.819 or later is supported. To install ActivePerl on Windows:

1) Download the ActivePerl MSI from http://www.activestate.com/Products/ActivePerl/.

2) Run the ActivePerl Installer (accepting all defaults is fine).

You can also build Perl yourself (which requires a C compiler) or download one of the other binary distributions. The Perl source for building it yourself is available from CPAN, as are a few other binary distributions that are alternatives to ActiveState. This approach is not recommended unless you have specific reasons for doing so and know what you're doing. If that's the case you probably don't need to be reading this guide.

Cygwin is a UNIX emulation environment for Windows and comes with its own copy of Perl.

Information on Cygwin and Bioperl is found below.

[edit] Bioperl on Windows

Perl is a programming language that has been extended a lot by the addition of external modules.

These modules work with the core language to extend the functionality of Perl.

Bioperl is one such extension to Perl. These modular extensions to Perl sometimes depend on the functionality of other Perl modules and this creates a dependency. You can't install module X unless you have already installed module Y. Some Perl modules are so fundamentally useful that the Perl developers have included them in the core distribution of Perl - if you've installed Perl then these modules are already installed. Other modules are freely available from CPAN, but you'll have to install them yourself if you want to use them. Bioperl has such dependencies.

Bioperl is actually a large collection of Perl modules (over 1000 currently) and these modules are split into seven packages. These seven packages are:

Bioperl Group	Functions
bioperl (the core)	Most of the main functionality of Bioperl
bioperl-run	Wrappers to a lot of external programs
bioperl-ext	Interaction with some alignment functions and the Staden package
bioperl-db	Using Bioperl with BioSQL and local relational databases
bioperl-microarray	Microarray specific functions
bioperl-pedigree	manipulating genotype, marker, and individual data for linkage studies
bioperl-gui	Some preliminary work on a graphical user interface to some Bioperl functions

The Bioperl core is what most new users will want to start with. Bioperl (the core) and the Perl modules that it depends on can be easily installed with the perl package Manager PPM. PPM is an ActivePerl utility for installing Perl modules on systems using ActivePerl. PPM will look online (you have to be connected to the internet of course) for files (these files end with .ppd) that tell it how to install the modules you want and what other modules your new modules depends on. It will then download and install your modules and all dependent modules for you.

These .ppd files are stored online in PPM repositories. ActiveState maintains the largest PPM repository and when you installed ActivePerl PPM was installed with directions for using the ActiveState repositories. Unfortunately the ActiveState repositories are far from complete and other ActivePerl users maintain their own PPM repositories to fill in the gaps. Installing will require you to direct PPM to look in three new repositories as detailed in Installation Guide.

Once PPM knows where to look for Bioperl and it's dependencies you simply tell PPM to search for packages with a particular name, select those of interest and then tell PPM to install the selected packages.

[edit] Beyond the Core

You may find that you want some of the features of other Bioperl groups like bioperl-ext or bioperl-pipeline. Currently, plans include setting up PPM packages for installing these parts of Bioperl; check this by doing a Bioperl search in PPM. If these are not available, though, you can use the following instructions for installing the other distributions.

For bioperl-run, bioperl-db and bioperl-network v1.5.2 or higher you can use the PPD or CPAN installation instructions above. For other packages you will need nmake (see also the CPAN installation instructions), and a willingness to experiment. You'll have to read the installation documents for each component that you want to install, and use nmake where the instructions call for make, like so:

perl Makefile.PL
nmake
nmake test
nmake install

nmake test will likely produce lots of warnings, many of these can be safely ignored. You will have to determine from the installation documents what dependencies are required, and you will have to get them, read their documentation and install them first. It is recommended that you look through the PPM repositories for any modules before resorting to using nmake as there isn't any guarantee modules built using nmake will work. The details of this are beyond the scope of this guide. Read the documentation. Search Google. Try your best, and if you get stuck consult with others on the BioPerl mailing list.

[edit] Setting environment variables

Some modules and tools such as Template:PM and clustal_w, require that environment variables are set; a few examples are listed here. Different versions of Windows utilize different methods for setting these variables. NOTE: The instructions that comes with the BLAST executables for setting up BLAST on Windows are out-of-date. Go to the following web address for instructions on setting up standalone BLAST for Windows: http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/pc_setup.html

• For Windows XP, go here. This does not require a reboot but all active shells will not reflect any changes made to the environment.
• For older versions (Windows 95 to ME), generally editing the C:\autoexec.bat file to add a variable works. This requires a reboot. Here's an example:

set BLASTDB=C:\blast\data

For either case, you can check the variable this way:

C:\Documents and Settings\Administrator>echo %BLASTDB%
C:\blast\data

Some versions of Windows may have problems differentiating forward and back slashes used for directories. In general, always use backslashes (\). If something isn't working properly try reversing the slashes to see if it helps.

For setting up Cygwin environment variables quirks, see an example below.

[edit] Installing bioperl-db

bioperl-db now works for Windows w/o installing CygWin. This has primarily been tested on WinXP using MySQL5, but it is expected that other bioperl-db supported databases (PostgreSQL, Oracle) should work.

You will need Bioperl 1.5.2, a relational database (I use MySQL5 here as an example), and the Perl modules Template:CPAN and Template:CPAN, which can be installed from PPM as desribed above (make sure the addidtional repositories for Kobes and Bribes are added, they will have the latest releases). Do NOT try using nmake with these modules as they will not build correctly under Windows! The PPM builds, by Randy Kobes, have been modified and tested specifically for Windows and ActivePerl.

NOTE: we plan on having a PPM for bioperl-db available along with the regular bioperl 1.5.2 release PPM. We will post instructions at that time on using PPM to install bioperl-db.

to begin, follow instructions detailed in the Installation Guide for adding the three new repositories (Bioperl, Kobes and Bribes). Then install the following packages:

1) DBI

2) DBD-mysql

The next step involves creating a database. The following steps are for MySQL5:

>mysqladmin -u root -p create bioseqdb
Enter password: **********

The database needs to be loaded with the BioSQL schema, which can be downloaded as a tarball here.

>mysql -u root -p bioseqdb < biosqldb-mysql.sql
Enter password: **********

Download bioperl-db from the anonymous Subversion repository. Use the following to install the modules:

perl Makefile.PL
nmake

Now, for testing out bioperl-db, make a copy of the file DBHarness.conf.example in the bioperl-db test subdirectory (bioperl-db\t). Rename it to DBHarness.biosql.conf, and modify it for your database setup (particularly the user, password, database name, and driver). Save the file, change back to the main bioperl-db directory, and run 'nmake test'. You may see lots of the following lines,

....
Subroutine Bio::Annotation::Reference::(eq redefined at C:/Perl/lib/overload.pm line 25, 
    <GEN0> line 1.
Subroutine new redefined at C:\Perl\src\bioperl\bioperl-live/Bio\Annotation\Reference.pm line 80,
    <GEN0> line 1.
....

which can be safely ignored (These come from ActivePerl's excessively paranoid -w flag). All tests should pass. NOTE : tests should be run with a clean database with the BiOSQL schema loaded, but w/o taxonomy loaded (see below).

To install, run:

nmake install

It is recommended that you load the taxonomy database using the script load_ncbi_taxonomy.pl included in biosql-schema\scripts. You will need to download the latest taxonomy files. This can be accomplished using the -download flag in load_ncbi_taxonomy.pl, but it will not 'untar' the file correctly unless you have GNU tar present in your PATH (which most Windows users will not have), thus causing the following error:

>load_ncbi_taxonomy.pl -download -driver mysql -dbname bioseqdb -dbuser root -dbpass **********
The system cannot find the path specified.
Loading NCBI taxon database in taxdata:
        ... retrieving all taxon nodes in the database
        ... reading in taxon nodes from nodes.dmp
Couldn't open data file taxdata/nodes.dmp: No such file or directory rollback ineffective with 
AutoCommit enabled at C:\Perl\src\bioperl\biosql-schema\scripts\load_ncbi_taxonomy.pl line 818.
Rollback ineffective while AutoCommit is on at 
C:\Perl\src\bioperl\biosql-schema\scripts\load_ncbi_taxonomy.pl line 818.
rollback failed: Rollback ineffective while AutoCommit is on

Use a file decompression utility like 7-Zip to 'untar' the files in the folder (if using 7-Zip, this can be accomplished by right-clicking on the file and using the option 'Extract here'). Rerun the script without the -download flag to load the taxonomic information. Be patient, as this can take quite a while:

>load_ncbi_taxonomy.pl -driver mysql -dbname bioseqdb -dbuser root -dbpass **********

Loading NCBI taxon database in taxdata:
        ... retrieving all taxon nodes in the database
        ... reading in taxon nodes from nodes.dmp
        ... insert / update / delete taxon nodes
        ... (committing nodes)
        ... rebuilding nested set left/right values
        ... reading in taxon names from names.dmp
        ... deleting old taxon names
        ... inserting new taxon names
        ... cleaning up
Done.

Now, load the database with your sequences using the script load_seqdatabase.pl, in bioperl-db's bioperl-db\script directory:

C:\Perl\src\bioperl\bioperl-db\scripts\biosql>load_seqdatabase.pl -drive mysql 
                              -dbname bioseqdb -dbuser root -dbpass **********
Loading NP_249092.gpt ...
Done.

You may see occasional errors depending on the sequence format, which is a non-platform-related issue. Many of these are due to not having an updated taxonomic database and may be rectified by updating the taxonomic information as detailed in load_ncbi_taxonomy.pl's POD.

Thanks to Baohua Wang, who found the initial Windows-specific problem in Template:PM that led to this fix, to Sendu Bala for fixing Template:Bugzilla, and to Hilmar Lapp for his input.

[edit] Bioperl in Cygwin

Cygwin is a Unix emulator and shell environment available free at http://www.cygwin.com. Bioperl v. 1.* runs well within Cygwin. 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 files to that directory. To uninstall Cygwin just delete that directory.

One advantage of using Bioperl in Cygwin is that all the external modules are available through CPAN - the same cannot be said of ActiveState's PPM utility.

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 (for example, THE BIOPERL BUNDLE and INSTALLING BIOPERL THE EASY WAY USING CPAN).

[edit] bioperl-db in Cygwin

This package is installed using the instructions contained in the package, without modification. Since postgres is a package within Cygwin this is probably the easiest of the 3 platforms supported in bioperl-db to install (postgres, Mysql, Oracle).

[edit] Cygwin tips

If you can, install Cygwin on a drive or partition that's NTFS-formatted, not FAT32-formatted. When you install Cygwin on a FAT32 partition you will not be able to set permissions and ownership correctly. In most situations this probably won't make any difference but there may be occasions where this is a problem.

If you're trying to use some application or resource outside of 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 up with paths written in these different syntaxes, depending.

[edit] MySQL and DBD::mysql

You may want to install a relational database in order to use BioPerl db, BioSQL or OBDA. The easiest way to install Mysql is to use the Windows binaries available at http://www.mysql.com. Note that Windows does not have sockets, so you need to force the Mysql connections to use TCP/IP instead. Do this by using the -h, or host, option from the command-line. Example:

>mysql -h 127.0.0.1 -u <user> -p<password> <database>

Alternatively you could install postgres instead of MySQL, postgres is already a package in Cygwin.

One known issue is that Template:CPAN can be tricky to install in Cygwin and this module is required for the bioperl-db, Biosql, and bioperl-pipeline external packages. Fortunately there's some good instructions online:

• Instructions included with DBD::mysql
• Additional instructions if you run into any problems; this information is more up-to-date, covers post-2.9 DBD::mysql quirks in Cygwin.

[edit] Expat

Note that expat comes with Cygwin (it's used by the modules Template:CPAN and Template:CPAN, which are used by certain Bioperl modules).

[edit] Directory for temporary files

Set the environmental variable TMPDIR, programs like BLAST and clustalw need a place to create temporary files. e.g.:

setenv TMPDIR e:/cygwin/tmp     # csh, tcsh
export TMPDIR=e:/cygwin/tmp    # sh, bash

This is not the syntax that Cygwin understands, which would be something like /cygdrive/e/cygwin/tmp or /tmp, this is the syntax that a Windows application expects.

If this variable is not set correctly you'll see errors like this when you run Template:PM:

  ------------- EXCEPTION: Bio::Root::Exception -------------
  MSG: Could not open /tmp/gXkwEbrL0a: No such file or directory
  STACK: Error::throw
  ..........

[edit] BLAST

If you want use BLAST we recommend that the Windows binary be obtained from NCBI (ftp://ftp.ncbi.nih.gov/blast/executables/LATEST/ - the file will be named something like blast-2.2.13-ia32-win32.exe). Then follow the Windows instructions in README.bls. You will also need to set the BLASTDIR environment variable to reflect the directory which holds the blast executable and data folder. You may also want to set other variables to reflect the location of your databases and substitution matrices if they differ from the location of your blast executables; see Installing Bioperl for Unix for more details.

[edit] Compiling C code

Although we've recommended using the BLAST and MySQL binaries you should be able to compile just about everything else from source code using Cygwin's gcc. You'll notice when you're installing Cygwin that many different libraries are also available (gd, jpeg, etc.).