[Bioperl-l] install 1.2.1 help newbie
Julian Dow
j.a.t.dow at bio.gla.ac.uk
Mon Jun 23 22:07:21 EDT 2003
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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