[Bioperl-l] install 1.2.1 help newbie
Brian Osborne
brian_osborne at cognia.com
Wed Jun 25 10:05:45 EDT 2003
Julian,
I must apologize, I actually cannot help you but I can make a suggestion. If
you working on Windows and really want to use Bioperl you may find life
easier using it within the Unix emulator Cygwin. I'm sure there are adepts
out there who are happily using Activestate Perl and Bioperl but there are
also those like yourself who are finding installation quite frustrating.
Even if you managed some of the steps you'd end up facing the fact that many
of external modules used by Bioperl aren't supplied by Activestate's PPMs,
perhaps never will be.
Cygwin advantages:
Free.
Fast and easy installation.
Free gcc, and hundreds of Unix utilities
Bioperl installs as easily on Cygwin as on the Unix's
Every bit of Perl is available
Choice of bash, tcsh, zsh
Fast. Or as fast as Windows.
Disadvantages:
Not every Unix capability is present in Cygwin
Some of the compiles are tricky (e.g. DBD::Oracle, DBD::Mysql, gd)
Need to know some Unix
Likes to be installed on NTFS, not FAT32
Not the deepest or most "technical" evaluation, I know!
The truth is that Bioperl has never done good Activestate support, it seems
that none of the "regulars" on this list use it, or have to time to address
specific installation problems. By contrast Cygwin and Bioperl "just work",
at least for me. And I should add that I can do serious work in Cygwin, big
sequence files, big indices, big Mysql databases, and so on.
Brian O.
-----Original Message-----
From: bioperl-l-bounces at portal.open-bio.org
[mailto:bioperl-l-bounces at portal.open-bio.org]On Behalf Of Julian Dow
Sent: Monday, June 23, 2003 4:07 PM
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] install 1.2.1 help newbie
Dear bioperl
>General comments, suggestions and installation war stories should be sent
>to the project mail-list <mailto:bioperl-l at bioperl.org>bioperl-l.
OK, I'd appreciate help installing 1.2.1 into Activestate perl on Win XP.
On http://www.bioperl.org/Core/Latest/INSTALL.WIN
>1.3.2 ActiveState For PERL 5.8.0
>================================
>
>ppm> repository add bioperl http://bioperl.org/DIST
>ppm> search bioperl (shows available bioperl versions)
>
>This last command returns a numbered list of the available bioperl
>versions.
>Select the number of the version you wish to install and type:
>
>ppm> install <number>
>SO I tried:
> rep
>
> PPM3 will return something resembling this:
>
> Repositories:
> [1] ActiveCD
> [2] ActiveState Package Repository
> [ ] An inactive repository
>
> In the example above, entering 'rep off 2' will disable the second
> repository (the ActiveStat Package Repository). To add another
> repository:
>
> rep add [options] <NAME> <LOCATION>
>
> The following options are available for the 'add' command:
>
> * -username
>
> * -password
>
> These options allow you to specify a username and password to be used
> when logging into a repository. Currently, these are only used for FTP
> and WWW repositories.
>
> For example:
>
> rep add "EZE" http://foo.com/MyPPMPackages
>
> with "EZE" being the name of the repository (for easy reference) and
the
> location noted by the http location. If you were to enter the rep
> command again, you would see:
>
> ppm> rep
> Repositories:
> [1] ActiveCD
> [2] ActiveState Package Repository
> [3] EZE
> [ ] An inactive repository
>
> To move the new repository to the top of the Active list, you would
> type:
>
> ppm> rep up EZE
> Repositories:
> [1] ActiveCD
> [2] EZE
> [3] ActiveState Package Repository
> [ ] An inactive repository
> ppm> rep up EZE
> Repositories:
> [1] EZE
> [2] ActiveCD
> [3] ActiveState Package Repository
> [ ] An inactive repository
>
> To disable the ActiveCD repository temporarily, enter the following:
>
> ppm> rep off ActiveCD
> Repositories:
> [1] EZE
> [2] ActiveState Package Repository
> [ ] ActiveCD
> [ ] An inactive repository
>
> To describe a repository, refer to it either by name, or by the number
> displayed next to the repository in the Active Repositories list. You
> must refer to inactive repositories by their full name.
>
> ppm> rep describe 2
> Describing Active Repository 2:
> Name: ActiveState Package Repository
> Location: http://ppm.ActiveState.com/cgibin/PPM/...
> Type: PPMServer 2.00
> ppm> rep describe ActiveCD
> Describing Inactive Repository:
> Name: ActiveCD
> Location: F:\PPMPackages\5.8plus
> Type: Local Directory
>
> To re-activate the ActiveCD repository, use the *rep on* command. You
> must refer to inactive repositories by name, not number.
>
> ppm> rep on ActiveCD
> Active Repositories:
> [1] EZE
> [2] ActiveState Package Repository
> [3] ActiveCD
> [ ] An inactive repository
>
> Repository Types
> PPM3 supports several types of package repositories:
>
> 1. PPM Server 3.0
>
> ActiveState's SOAP-driven package server. Because all searches are
> done server-side, the server can deliver much richer information
> about packages than other repositories.
>
> 2. PPM Server 2.0
>
> The SOAP server designed for PPM version 2. PPM3 ships with the
PPM2
> repository as well as the PPM3 repository, so you can use either.
> Simple searches are performed server-side. If your search is too
> complicated for the server, PPM3 will download the package summary
> and search by itself.
>
> 3. Web Repositories
>
> Older versions of PPM used non-SOAP repositories (directories full
> of PPD files accessible using a web browser). Over the history of
> PPM, there have been several different ways of organising the
files
> so that PPM can search for packages properly. PPM3 tries to
download
> a summary file first -- if that fails, it gets the directory
index.
> It parses the summary or the index, and caches it. Searches are
done
> from the cache.
>
> 4. FTP Repositories
>
> FTP is another way of exposing a directory full of PPD files. PPM3
> consideres FTP repositories a subset of Web repositories. Treat
them
> as identical: PPM3 downloads the summary or the "index" (file
> listing in this case), parses it, and then searches from it.
>
> 5. Local Repositories
>
> To support installing packages from the ActiveCD, a local
directory
> can be a repository. PPM3 searches the files in the directory. All
> valid path formats are supported, including UNC paths.
>ppm> search 1 *
>No such search result set '1'.
>ppm> rep off 2
>Repositories:
>[1] Bioperl
>[2] ActiveState Package Repository
>[ ] ActiveState PPM2 Repository
>ppm> rep off 3
>Error: no such active repository 3
>ppm> rep off 2
>Repositories:
>[1] Bioperl
>[ ] ActiveState Package Repository
>[ ] ActiveState PPM2 Repository
>ppm> search *
>Searching in Active Repositories
>Missing base argument at C:/Perl/site/lib/PPM/Repository.pm line 174
>
>C:\Perl>ppm
>PPM - Programmer's Package Manager version 3.0.1.
>Copyright (c) 2001 ActiveState SRL. All Rights Reserved.
>
>Entering interactive shell. Using Term::ReadLine::Stub as readline library.
>
>Profile tracking is not enabled. If you save and restore profiles manually,
>your profile may be out of sync with your computer. See 'help profile' for
>more information.
>
>Type 'help' to get started.
>
>ppm> rep
>Repositories:
>[1] Bioperl
>[ ] ActiveState Package Repository
>[ ] ActiveState PPM2 Repository
>ppm> rep on 2
>Error: no such inactive repository '2'
>ppm> rep on *
>Error: no such inactive repository '*'
>ppm> rep on Activestate
>Repositories:
>[1] Bioperl
>[2] ActiveState PPM2 Repository
>[ ] ActiveState Package Repository
>ppm> rep on activestate
>Error: no such inactive repository 'ActiveState PPM2 Repository'
>ppm> search ppm
>Searching in Active Repositories
>Missing base argument at C:/Perl/site/lib/PPM/Repository.pm line 174
>
>C:\Perl>rep desc 1
>'rep' is not recognized as an internal or external command,
>operable program or batch file.
>
>C:\Perl>ppm
>PPM - Programmer's Package Manager version 3.0.1.
>Copyright (c) 2001 ActiveState SRL. All Rights Reserved.
>
>Entering interactive shell. Using Term::ReadLine::Stub as readline library.
>
>Profile tracking is not enabled. If you save and restore profiles manually,
>your profile may be out of sync with your computer. See 'help profile' for
>more information.
>
>Type 'help' to get started.
>
>ppm> rep desc 1
>Describing Active Repository 1:
> Name: Bioperl
>Location: http://bioperl.org/DIST/
> Type: Webpage
>ppm> rep remove 1
>No such repository command 'remove'; see 'help repository'.
>ppm> help repository
>repository -- Repository Control
> Synopsis
> rep Displays all repositories
> rep add [name] <location> Adds a new repository; makes it active
> rep delete <name or num> Deletes specified repository
> rep describe <name or num> Displays information about the specified
> repository
> rep rename <name or num> <name>
> Renames the specified repository to
> the given name
> rep on <name> Activates the specified repository
> rep off <name or num> Removes the repository from the active
list
> rep up <name or num> Moves the specified repository up one
> rep down <name or num> Moves the specified repository down one
>
> Description
> The *repository* (or *rep*) command controls two lists or
repositories:
>
> 1 The list of "active" repositories. This is the list of
repositories
> used by *search*, *install*, *upgrade*, and *verify*.
>
> 2 The list of all known repositories. You can designate a repository
> "inactive", which means PPM will not use it in any commands.
>
> If no arguments are given, the rep command will list the active
> repositories defined in the PPM settings. The order is significant:
when
> installing a package, PPM will try the first repository, then the
> second, and so on, until it find the package you asked for. When
> searching, PPM merges the results of all the repositories together, so
> the order is less important (see the *search* command).
>
> For example, when you enter:
>
> rep
>
> PPM3 will return something resembling this:
>
> Repositories:
> [1] ActiveCD
> [2] ActiveState Package Repository
> [ ] An inactive repository
>
> In the example above, entering 'rep off 2' will disable the second
> repository (the ActiveStat Package Repository). To add another
> repository:
>
> rep add [options] <NAME> <LOCATION>
>
>
>ppm> rep delete 1
>Repositories:
>[1] ActiveState PPM2 Repository
>[ ] ActiveState Package Repository
>ppm> repository add Bioperl http://bioperl.org/DIST
>Repositories:
>[1] ActiveState PPM2 Repository
>[2] Bioperl
>[ ] ActiveState Package Repository
>ppm> rep off 1
>Repositories:
>[1] Bioperl
>[ ] ActiveState Package Repository
>[ ] ActiveState PPM2 Repository
>ppm> search *
>Searching in Active Repositories
> 1. Bioperl-1.2 [1.2] Bioperl 1.2 PPM3 Archive
> 2. Bioperl-1.2.1 [1.2.1] Bioperl 1.2.1 PPM3 Archive
> 3. Text-Shellwords [1.00] Text::Shellwords - Parse lines into tokens
> like t~
>ppm> install 2
>Package 2:
>Error: Failed to download URL http://bioperl.org/DIST/File-Temp.ppd:
>404 Not Found
>ppm> install 1
>Package 1:
>Error: Failed to download URL http://bioperl.org/DIST/File-Temp.ppd:
>404 Not Found
>ppm> rep
>Repositories:
>[1] Bioperl
>[ ] ActiveState Package Repository
>[ ] ActiveState PPM2 Repository
>ppm> search bioperl
>Searching in Active Repositories
> 1. Bioperl-1.2 [1.2] Bioperl 1.2 PPM3 Archive
> 2. Bioperl-1.2 [1.2] Bioperl 1.2 PPM3 Archive
> 3. Bioperl-1.2.1 [1.2.1] Bioperl 1.2.1 PPM3 Archive
> 4. Bioperl-1.2.1 [1.2.1] Bioperl 1.2.1 PPM3 Archive
>ppm> install 3
>Package 3:
>Error: Failed to download URL http://bioperl.org/DIST/File-Temp.ppd:
>404 Not Found
>ppm> install 4
>Package 4:
>Error: Failed to download URL http://bioperl.org/DIST/File-Temp.ppd:
>404 Not Found
>ppm>
Is the repository at fault, or me? :-)
Now I was trying to do this because I thought I had successfully installed
1.2.1, but when I tried 'use Bio::tools' it couldn't be found. True enough,
in Bioperl\tools\run I found the readme:
> This directory is now mainly in bioperl-run package
>which you should install alongside Bioperl to get over
>50 different runnable options. We might decide to merge
>the two packages again, but the feeling is that bioperl
>"core" is getting a little too big.
>
> Bioperl-run follows the same release tagging schedule
>as Bioperl. Pick it up from www.bioperl.org and/or CPAN
SO what I had been hoping to find at the bioperl archive was bioperl-run,
but that doesn't seem to be on the repository list. Am I looking in the
wrong place? I only wanted to find pest sequences...
regards, Julian Dow
------------------------------------------------------------------
Prof. Julian A.T. Dow IBLS Division of Molecular Genetics,
University of Glasgow, Glasgow G11 6NU, UK
Phone: +44 141 330 4616 FAX: +44 141 330 4878
email: j.a.t.dow at bio.gla.ac.uk WWW: fly.to/tubules
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