[Bioperl-l] New Jekyll theme at bioperl.github.io

[Fields, Christopher J]

BioJava and BioSQL would be the only other ones I can think of.  EMBOSS is static web content for the most part if I recall; is that hosted on the AWS server or is it a redirect?

chris

On Jan 10, 2016, at 2:26 AM, Peter Cock <p.j.a.cock at googlemail.com<mailto:p.j.a.cock at googlemail.com>> wrote:

On Sat, Jan 9, 2016 at 7:03 AM, Brian Osborne <bosborne11 at verizon.net<mailto:bosborne11 at verizon.net>> wrote:
Peter,

It looks like you have a very nice plan to migrate this content that is
close to - if not fully - automated. Good idea.

Personally, the way I was thinking about the BioPerl Wiki was a bit
different. The BioPerl Wiki is quite old, quite large, and a lot of its
content is dated, or wrong, or now superfluous (e.g. each module in BioPerl
has a Wiki page, which was written by code, and there are many Wiki pages
about applications or terms or formats that are now handled by Wikipedia).
So this migration, again my personal view, was an opportunity to remove a
lot of content yet preserve what was truly useful. Also bear in mind that
resources are very stretched at BioPerl, the less content we have to
maintain, the better. So we hand selected the pages we wanted to migrate,
and we also did some amount of editing of _each_ selected page, and
consolidated pages. So that process gave us a set of some 150 GFM pages. No
versions.

Fair enough - I'd have opted for a full automated conversion (to
capture the contributor history), and then done the clean up -
but the key thing is you've done this. Chatting with Chris Fields
there is certainly a lot of good stuff on the old BioPerl wiki which
would be better placed somewhere central (e.g. file formats on
wikipedia?).

Then the question I puzzled over was “what look?” Check these out, if you
want to get a sense of your Jekyll options:

http://jekyllthemes.org<http://jekyllthemes.org/>
https://github.com/jekyll/jekyll/wiki/sites

There is necessarily some editing involved in the migration. Hopefully most
of GFM does not have to be touched, (and the “front matter” section that
Jekyll wants can be added by script to the GFM pages) but the migrators will
have to look at the “topmost" pages (and maybe there’s just one of these,
index.html or index.md).

Yes - and likely categories would work that way too.

You also will want search capabilities in some of these sites. Some themes
have it already, most of these above do not.

Interesting - I'd not looked at that at all.

There also appears to be an issue around Google searching if sitemap.xml is
not right, have not looked into this yet:

http://gon.to/2015/03/03/f-percent-number-ck-github-pages-for-jekyll-why-i-decided-to-use-digital-ocean/

Anyway, having said all of that, I can assist with the migration. What is
the full list of Wikis? Is it something like this?

[bosborne at ip-10-116-249-158 ~]$ ls /obf/websites/
biodas.org           biopathways.org  bioruby.org  cgi.biodas.org
helpdesk.open-bio.org  www.arareko.net
biojava.org          bioperl.org      biosoap.org  cross-site-stuff
lists.open-bio.org     www.open-bio.org
biolib.open-bio.org  bioprolog.org    biosql.org   doc.bioperl.org
news.open-bio.org
biomoby.org          biopython.org    blipkit.org  emboss.open-bio.org
obda.open-bio.org

Some of these are not Wikis, like biomoby and open-bio.org.

BioMoby has some complicated stuff, but www.open-bio.org<http://www.open-bio.org/> does
have a wiki (which I'm looking at as the first migration) and some
static HTML pages like old BOSC conferences (hopefully they
can be moved into GitHub as static HTML pages).

And do we have owners for all of these? Are some of no interest?

Hopefully - migration is a good chance to verify all that.

Finally, I think that each of these needs its own GitHub account
in order to get a GitHub Pages site. Or were you thinking of only
migrating some of these? A bunch of questions for OBF here.

Yes, but most of the active projects already have GitHub accounts.
We're looking at BioPerl (you), the main OBF wiki and Biopython
(me) as the first trial migrations to GitHub pages.

Regards,

Peter

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