These are chat archives for biojs/biojs

6th
Feb 2015
Sebastian Wilzbach
@wilzbach
Feb 06 2015 00:00
so there is a huge codebase
Prasun Anand
@prasunanand
Feb 06 2015 00:00
Last year I tried to copy this website http://browse.yeastgenome.org/fgb2/gbrowse/scgenome/ for my college project
:worried:
I couldn't do it
So which are the easy ones
Sebastian Wilzbach
@wilzbach
Feb 06 2015 00:00
I dont want to stop you working on it
This was just a warning
Prasun Anand
@prasunanand
Feb 06 2015 00:01
Ok then I'll try them later
:)
So which are the easy ones to start with
Sebastian Wilzbach
@wilzbach
Feb 06 2015 00:01
e.g. biojs/biojs#134
biojs/biojs#132
maybe biojs/biojs#118
Prasun Anand
@prasunanand
Feb 06 2015 00:03
I'' do biojs/biojs#132
Plasmids are interesting
:)
Sebastian Wilzbach
@wilzbach
Feb 06 2015 00:07
Afaik
Prasun Anand
@prasunanand
Feb 06 2015 00:08
:)
Where should i start then?
Sebastian Wilzbach
@wilzbach
Feb 06 2015 00:09
There is one component that tries to display plasmids
But I haven't looked at it for a long time, so I don't know how usable it really is
But could be a starting point for inspiration or improvement
Prasun Anand
@prasunanand
Feb 06 2015 00:11
Hmmm, it doesn't display any annotated information
I'll do it.
Sebastian Wilzbach
@wilzbach
Feb 06 2015 00:19
Wow you are highly motivated :)
Just let us know when you need help
Prasun Anand
@prasunanand
Feb 06 2015 00:22
:) I'll start working then.
Prasun Anand
@prasunanand
Feb 06 2015 00:31
@greenify . Should I start from scratch or from https://github.com/jmVillaveces/biojs-vis-circularfv
and I also want to know what should we finally end up with. (features provided)
Prasun Anand
@prasunanand
Feb 06 2015 00:44
and sorry Annotation feature is there
:)
tyreek
@tyreek
Feb 06 2015 10:00
(biojs-registry via irc) BioJS package update: biojs-sniper to 0.2.5 by @greenify
tyreek
@tyreek
Feb 06 2015 11:25
(TanujS via irc) basically what are we trying to achieve in the project ipython+galaxy.
Sebastian Wilzbach
@wilzbach
Feb 06 2015 12:35
@prasunanand: I would suggest you play a bit with it
I just remember that there is another beautiful plasmid representation: http://angularplasmid.vixis.com/ (source: https://github.com/vixis/angularplasmid)
we could also work on getting this into BiojS :)
tyreek
@tyreek
Feb 06 2015 12:45
(TanujS via irc) greencow: Thank you so much! I would revert back for more enquiry :p
@greenify I want to populate the left navbar with links to all the tutorial pages. I am getting errors. I don't understand the code.
This message was deleted
Sebastian Wilzbach
@wilzbach
Feb 06 2015 17:01
which error do you get?
the pastebin is just the html code
do you mind to use the DNA logo from the registry?
Prasun Anand
@prasunanand
Feb 06 2015 17:02
Regenerating: 1 files at 2015-02-06 16:02:46 Liquid Exception: tag does not expect else tag in _layouts/container.html
...error:
Error: tag does not expect else tag
Error: Run jekyll build --trace for more information.
DNA logo?
Sebastian Wilzbach
@wilzbach
Feb 06 2015 17:02
on biojs.io
Prasun Anand
@prasunanand
Feb 06 2015 17:02
ok
Sebastian Wilzbach
@wilzbach
Feb 06 2015 17:03
it is liquid
and the error is quite obvious
" tag does not expect else tag "
Prasun Anand
@prasunanand
Feb 06 2015 17:04
But still getting errors
Sebastian Wilzbach
@wilzbach
Feb 06 2015 17:05
btw yes I have written that code ..
(on a night - sorry)
if you really dont understand it - remove pieces until it is working again
and then reinsert until it fails
Prasun Anand
@prasunanand
Feb 06 2015 17:07
OK. i'll try that. Do I need to edit pagination.rb and sorted_for.rb
Sebastian Wilzbach
@wilzbach
Feb 06 2015 17:07
nope normally not
they are not causing your error!
Prasun Anand
@prasunanand
Feb 06 2015 17:08
I am getting the list in tutorials page but not in homepage.
Sebastian Wilzbach
@wilzbach
Feb 06 2015 17:09
homepage = start page?
Prasun Anand
@prasunanand
Feb 06 2015 17:09
yes
Sebastian Wilzbach
@wilzbach
Feb 06 2015 17:09
did you remove essential parts?
Prasun Anand
@prasunanand
Feb 06 2015 17:09
Nah,
Sebastian Wilzbach
@wilzbach
Feb 06 2015 17:10
{% sorted_keys_for el in site.series sort_by:sort has_hash:site.series %}
{% if site.series[el].displayed %}
<h4> <a href="/series/{{ el }}/index.html"> {{ site.series[el].desc }} </a> </h4>
{% endif %}
{% endsorted_keys_for %}
that is the entire listing
if you haven't modified the yaml and the pages are still there this will work ..
Prasun Anand
@prasunanand
Feb 06 2015 17:10
cool
Sebastian Wilzbach
@wilzbach
Feb 06 2015 17:11
(this is the code from index.md)
Prasun Anand
@prasunanand
Feb 06 2015 17:13
I am not getting it. Need to spend sometime on it
:)
Sebastian Wilzbach
@wilzbach
Feb 06 2015 17:13
let me know if you need more help
Prasun Anand
@prasunanand
Feb 06 2015 17:14
sure
got it. I mixed up _layouts/container.html and index.md .
Sebastian Wilzbach
@wilzbach
Feb 06 2015 17:18
every page extends a layout
however index.md is really only index.html
Prasun Anand
@prasunanand
Feb 06 2015 17:19
Yeah. :) I have placed a footer in the website. What should its contents be?
Sebastian Wilzbach
@wilzbach
Feb 06 2015 17:38
if you don't know what to put into it - than there is probably no need for it?
Prasun Anand
@prasunanand
Feb 06 2015 17:50
I think I can place links to "Get Involved" as in biojs.net
Sebastian Wilzbach
@wilzbach
Feb 06 2015 17:50
probably it will just get messy :(
but try it .. ;-)
Prasun Anand
@prasunanand
Feb 06 2015 17:51
It will not :)