Talk:Getting BioPerl

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Installing versus getting

At some point the installing and getting Bioperl need to either be combined on a single page or more properly separated I think. The platform specific installation instructions - like INSTALL.WIN should be brought into the wiki I think. The text versions can probably live on in the CVS repository but maybe should be updated to just point to the wiki site. There are some easy ways to get the wiki text back out into a file which could a step in Making a BioPerl release. --jason stajich 14:52, 13 February 2006 (EST)

Should the INSTALL docs be on the wiki as one single page for all OS's or separate pages, one for each specific OS (UNIX, Win, Mac)? I looked at both INSTALL and INSTALL.WIN and they're broken up into various sections, so keeping them separate makes sense. My personal preference would be having separate pages or sections for each OS, with links from the FAQ or other pages. That way, any platform-specific changes or additions (like installing Bioperl-db and BioSQL, platform-specific issues, etc) could be made relatively easily on each specific page or section and links can be made to them from the appropriate pages (like bioperl-db). --Chris Fields 16:06, 13 February 2006 (EST)
I say a separate page for each OS and just link them in assuming there is enough text to justify seperate pages. It might be simpler to start with just a single page with sections and we can break it out into sub-pages where it seems long enough. We started a Tutorial:Installing Perl modules to explain perl module installation generally from the different OSes perspectives too and this is all contained in a single page for now. --jason stajich 16:26, 13 February 2006 (EST)
I'll create a link from Getting BioPerl and try getting INSTALL.WIN into some wiki-shape. It may take a bit of time; I'm pretty busy this week with benchwork. --Chris Fields 16:40, 13 February 2006 (EST)

Windows installation files added, UNIX next?

I added the INSTALL.WIN file to the wiki and updated as much as I can this week. Wasn't too bad; I squeezed a lot of the edits in between benchwork. Also added a section on getting bioperl-db up and running on Windows, which is something I had written up for Hilmar but felt it needed to be included here. Brian has been cleaning up/adding links to the Cygwin portion of the page as well (which is good as Cygwin is definitely not my strong suit). Should I add the UNIX INSTALL file as well, at least get it in a decent format for everybody to mess with? --Chris Fields 00:23, 15 February 2006 (EST)

Yes, but along with all of this we need to remove the INSTALL and INSTALL.WIN files from the package, or figure out how to get the Wiki text back into the text files in the package. I prefer the latter approach myself as it's certainly standard to have a file called something like "INSTALL" in the package that you download. BIO 10:11, 15 February 2006 (EST)

Sounds good. Jason mentioned above he thought INSTALL and INSTALL.WIN should be modified to point the user back to the wiki which I think is more helpful (includes all the links and so on). If we plan on keeping both INSTALL docs with the distribution as plain text, are we going to somehow autogenerate the files every week? --Chris Fields 10:31, 15 February 2006 (EST)

Autogenerating a text version of a page is possible. Jason pointed out this WWW::Mediawiki::Client module, it has a get_server_page method that returns text, given a page. BIO 16:50, 15 February 2006 (EST)

I may give it a try using the installation pages here. Let you know how it goes. --Chris Fields 18:07, 15 February 2006 (EST)

UNIX Install page added

Added link from Getting BioPerl page for Installing Bioperl for Unix wiki page. Did some minor work on it, including adding tables. Needs major work (I didn't add any links, just ran out of time, no explicit code tags, but is in okay condition for now). --Chris Fields 11:46, 15 February 2006 (EST)

<bash> Vs. <pre> tags

I think the point of the <bash> tag was precisely to distinguish shell code from fixed width text. I don't remember very well if there was a talk about the use of <bash> or <pre> in cases like these. -- Mauricio 16:31, 5 July 2007 (EDT)

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