From 05da852fd02c09b2533adfb9ff92ecc09198b4e8 Mon Sep 17 00:00:00 2001 From: Brian Osborne Date: Fri, 11 Dec 2015 09:44:23 -0500 Subject: [PATCH] Update, matches the Web site version --- INSTALL.WIN | 899 +++++++++++++++--------------------------------------------- 1 file changed, 227 insertions(+), 672 deletions(-) rewrite INSTALL.WIN (83%) diff --git a/INSTALL.WIN b/INSTALL.WIN dissimilarity index 83% index 82e3efc6f..f6af650cf 100644 --- a/INSTALL.WIN +++ b/INSTALL.WIN @@ -1,672 +1,227 @@ -# $Id$ - - Installing Bioperl on Windows - - Contents - - * 1 Introduction - * 2 Requirements - * 3 Installation using the ActiveState Perl Package Manager - - * 3.1 GUI Installation - * 3.2 Comand-line Installation - - * 4 Installation using CPAN or manual installation - * 5 Bioperl - * 6 Bioperl on Windows - * 7 Beyond the Core - - * 7.1 Setting environment variables - * 7.2 Installing bioperl-db - - * 8 Bioperl in Cygwin - * 9 bioperl-db in Cygwin - * 10 Cygwin tips - * 11 MySQL and DBD::mysql - * 12 Expat - * 13 Directory for temporary files - * 14 BLAST - * 15 Compiling C code - -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. - - An up-to-date version of this document can be found on the BioPerl wiki: - - http://www.bioperl.org/wiki/Installing_Bioperl_on_Windows - -Requirements - - There are a couple of ways of installing Perl on a Windows machine. One is - to get the most recent build from Strawberry Perl, and the other is to get - it from ActiveState; both are software companies that provides free builds - of Perl for Windows users, but Strawberry Perl is recommended since is more - CPAN friendly because it includes a compiler (gcc), related tools and other - external libraries. The current (March 2014) build is 5.18.2. - - NOTE - Only Perl >= 5.8.8.819 is supported by the BioPerl team. Earlier - versions may work, but we do not support them. Perl 5.18 also works. 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 Perl on Windows: - - 1) Download the Strawberry Perl MSI from - http://strawberryperl.com/releases.html or ActivePerl MSI from - http://www.activestate.com/activeperl/downloads. - - 2) Run the 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. - -Installation using the ActiveState Perl Package Manager - - 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). NOTE - The DB_File installed with ActivePerl - 5.10 and above is a stub (i.e. it does not work). The Trouchelle - database below has a working DB_File. - - Repositories to add - +----------------------------------------------------------------+ - | Name | Location | - |--------------------------+-------------------------------------| - |BioPerl-Release Candidates|http://bioperl.org/DIST/RC | - |--------------------------+-------------------------------------| - |BioPerl-Regular Releases |http://bioperl.org/DIST | - |--------------------------+-------------------------------------| - |Kobes |http://theoryx5.uwinnipeg.ca/ppms | - |--------------------------+-------------------------------------| - |Bribes |http://www.Bribes.org/perl/ppm | - |--------------------------+-------------------------------------| - |Trouchelle |http://trouchelle.com/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. - - Comand-line Installation - - Use the ActiveState ppm-shell: - - 1) Open a cmd window by going to Start >> Run and typing - 'cmd' and pressing return. - - 2) Do - C:> ppm-shell - ppm> - - 3) Make sure you have the module PPM-Repositories. Try - installing it: - ppm> install PPM-Repositories - - 4) For BioPerl 1.6.1, we require at least the following - repositories. You may have some present already. - - ppm> repo add http://bioperl.org/DIST - ppm> repo add uwinnipeg - ppm> repo add trouchelle - - Because you have installed PPM-Repositories, PPM will know - your Perl version, and select the correct repo from the - table above. - - 5) Install BioPerl (not "bioperl"). - - ppm> install BioPerl - - If you are running ActiveState Perl 5.10, you may have a - glitch involving SOAP::Lite. Use the following workaround: - - 1) Get the index numbers for your active repositories: - - ppm> repo - - | id | pkgs | name | - | 1 | 11431 | ActiveState Package Repository | - | 2 | 14 | bioperl.org | - | 3 | 291 | uwinnipeg | - | 4 | 11755 | trouchelle | - - 2) Execute the following commands. (The session here is - based on the above table. Substitute the correct index - numbers for your situation.) - - rem -turn off ActiveState, trouchelle repos - ppm> repo off 1 - ppm> repo off 4 - rem -to get SOAP-Lite-0.69 from uwinnipeg... - ppm> install SOAP-Lite - rem -turn ActiveState, trouchelle back on... - ppm> repo on 1 - ppm> repo on 4 - rem -now try... - ppm> install BioPerl - -Installation using CPAN or manual installation - - When using ActivePerl, installation using PPM is preferred since it is - easier, but if you run into problems, or a PPM isn't available for the - latest version/package of BioPerl, or you want to choose which optional - dependencies to install, you can install manually by downloading the - appropriate package or by using CPAN (installation using CPAN will always - get you the latest version). Both manual methods ultimately need an - accessory compiling program like MinGW, which incorporates the necessary - tools like dmake and gcc. MinGW comes by default with Strawberry Perl, but - must be installed through PPM for ActivePerl. Also CPAN neeed to be upgraded - to >= v1.81, Module::Build to be installed (>= v0.2805) and Test::Harness to - be upgraded to >= v2.62: - - Dmake for ActivePerl - - 1) Install MinGW package through PPM: Using a cmd window type - 'ppm install MinGW' for 32bits Windows or 'ppm install MinGW64' for - 64bits Windows. Is IMPORTANT to check previously if ActiveState - provides the MinGW package for your ActivePerl version. For example, - although ActivePerl 5.18.2.1802 is currently available (May 2014), - the download page point mainly at ActivePerl 5.16.3.1604, and the - MinGW package is available for version 5.16 but NOT for version 5.18. - - CPAN for ActivePerl and Strawberry Perl - - 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'. - - 8) At the cpan> prompt, type 'install Test::Most'. - - You can now follow the unix instructions for installing using CPAN - (preferred), or install manually: - - 9) Download the .zip version of the package you want. - - 10) Extract the archive in the normal way. - - 11) 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' - - 12) Type 'perl Build.PL' and answer the questions appropriately. - - 13) 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. - - 14) Type 'perl Build install' to install Bioperl. - -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. - - 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. - -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. - -Beyond the Core - - You may find that you want some of the features of other Bioperl groups - like bioperl-run or bioperl-db. 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. - - Setting environment variables - - Some modules and tools such as Bio::Tools::Run::StandAloneBlast and - clustal_w, require that environment variables are set; a few examples - are listed in the INSTALL document. 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. - - 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 rel. 1.5.2, a relational database (I use MySQL5 here - as an example), and the Perl modules DBI and DBD::mysql, which - can be installed from PPM as desribed above (make sure the additional - 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 Git 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, - line 1. - Subroutine new redefined at C:\Perl\src\bioperl\bioperl-live/Bio\Annotation\Reference.pm line 80, - line 1. - .... - - which can be safely ignored (again, these come from ActivePerl's 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 - Bio::Root::Root that led to this fix, to Sendu Bala for fixing - Bug #1938, and to Hilmar Lapp for his input. - -Bioperl in Cygwin - - Cygwin is a Unix emulator and shell environment available free at - http://www.cygwin.com. Bioperl v. 1.* supposedly runs well within Cygwin, - though the latest release has not been tested with Cygwin yet. 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). - -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). - -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. - -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 -p - - Alternatively you could install postgres instead of MySQL, postgres is - already a package in Cygwin. - - One known issue is that DBD::mysql 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: - http://search.cpan.org/src/JWIED/DBD-mysql-2.1025/INSTALL.html#windows/cygwin - - * Additional instructions if you run into any problems; this - information is more up-to-date, covers post-2.9 DBD::mysql quirks in - Cygwin. - http://rage.against.org/installingdbdmysqlInCygwin - -Expat - - Note that expat comes with Cygwin (it's used by the modules - XML::Parser and XML::SAX::ExpatXS, which are used by certain - Bioperl modules). - -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 Bio::Tools::Run::StandAloneBlast: - - ------------- 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/blast+/LATEST/ - the file - will be named something like ncbi-blast-2.2.29+-win64.exe). Then follow the - Windows instructions from BLAST Help - (http://www.ncbi.nlm.nih.gov/books/NBK1762). 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. - -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.). + + Installing Bioperl on Windows + + Contents + + * 1 Introduction + * 2 Requirements + * 3 To install Perl on Windows + * 4 CPAN for ActivePerl and Strawberry Perl + * 5 Installation using CPAN or manual installation + * 6 Beyond the Core + * 7 Bioperl in Cygwin + +1 Introduction + +This installation guide was written by Barry Moore, Nathan Haigh and other Bioperl +authors based on the original work of Paul Boutros. + +Please report problems and fixes to the BioPerl mailing list, *bioperl-l* +(http://lists.open-bio.org/mailman/listinfo/bioperl-l). + +2 Requirements + +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), +and the other is to get it from ActiveState (http://www.activestate.com). Both +are software companies that provide free builds of Perl for Windows users, but +Strawberry Perl is recommended since it is more CPAN friendly and because it +includes a compiler (`gcc`) and related tools. + +3 To install Perl on Windows: + + 1) Download the Strawberry Perl MSI from + http://strawberryperl.com/releases.html or ActivePerl MSI from + http://www.activestate.com/activeperl/downloads. + 2) Run the 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. + +4 CPAN for ActivePerl and Strawberry Perl + + 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'. + + 8) At the cpan> prompt, type 'install Test::Most'. + +You can now follow the unix instructions for installing using CPAN (preferred), or install manually: + + 9) Download the .zip version of the package you want. + + 10) Extract the archive in the normal way. + + 11) 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' + + 12) Type 'perl Build.PL' and answer the questions appropriately. + + 13) 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. + + 14) Type 'perl Build install' to install Bioperl. + +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). NOTE - The DB_File installed with ActivePerl + 5.10 and above is a stub (i.e. it does not work). The Trouchelle + database below has a working DB_File. + + Repositories to add + +----------------------------------------------------------------+ + | Name | Location | + |--------------------------+-------------------------------------| + |BioPerl-Release Candidates|http://bioperl.org/DIST/RC | + |--------------------------+-------------------------------------| + |BioPerl-Regular Releases |http://bioperl.org/DIST | + |--------------------------+-------------------------------------| + |Kobes |http://theoryx5.uwinnipeg.ca/ppms | + |--------------------------+-------------------------------------| + |Bribes |http://www.Bribes.org/perl/ppm | + |--------------------------+-------------------------------------| + |Trouchelle |http://trouchelle.com/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. + 7) Click the green arrow (Run marked actions) to complete the + installation. + +Command-line Installation + + Use the ActiveState ppm-shell: + + 1) Open a cmd window by going to Start >> Run and typing + 'cmd' and pressing return. + + 2) Do + C:> ppm-shell + ppm> + + 3) Make sure you have the module PPM-Repositories. Try installing it: + ppm> install PPM-Repositories + + 4) For BioPerl 1.6.1, we require at least the following + repositories. You may have some present already. + + ppm> repo add http://bioperl.org/DIST + ppm> repo add uwinnipeg + ppm> repo add trouchelle + + Because you have installed PPM-Repositories, PPM will know + your Perl version, and select the correct repo from the + table above. + + 5) Install BioPerl (not "bioperl"). + + ppm> install BioPerl + + +5 Installation using CPAN or manual installation + +When using ActivePerl, installation using PPM is preferred since it is +easier, but if you run into problems, or a PPM isn't available for the +latest version/package of BioPerl, or you want to choose which optional +dependencies to install, you can install manually by downloading the +appropriate package or by using CPAN (installation using CPAN will always +get you the latest version). Both manual methods ultimately need an +accessory compiling program like MinGW, which incorporates the necessary +tools like dmake and gcc. MinGW comes by default with Strawberry Perl, but +must be installed through PPM for ActivePerl. Also CPAN neeed to be upgraded +to >= v1.81, Module::Build to be installed (>= v0.2805) and Test::Harness to +be upgraded to >= v2.62: + +Dmake for ActivePerl + + 1) Install MinGW package through PPM: Using a cmd window type + 'ppm install MinGW' for 32bits Windows or 'ppm install MinGW64' for + 64bits Windows. Is IMPORTANT to check previously if ActiveState + provides the MinGW package for your ActivePerl version. For example, + although ActivePerl 5.18.2.1802 is currently available (May 2014), + the download page point mainly at ActivePerl 5.16.3.1604, and the + MinGW package is available for version 5.16 but NOT for version 5.18. + +6 Beyond the Core + +You may find that you want some of the features of other Bioperl packages +like bioperl-run or bioperl-db. 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 + +7 Bioperl in Cygwin + +Cygwin is a Unix emulator and shell environment available free at +http://www.cygwin.com. It has been reported that Bioperl v. 1.* runs well +within Cygwin, though the latest release has not been tested with 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. + +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. + +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 +up with paths written in these different syntaxes, depending. + +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 -- 2.11.4.GIT