These are chat archives for biojs/biojs

17th
Feb 2015
rowlandm
@rowlandm
Feb 17 2015 02:49
Hi there
Sebastian Wilzbach
@wilzbach
Feb 17 2015 02:50
Cheers
rowlandm
@rowlandm
Feb 17 2015 02:50
I was just trying to get my head around all the new stuff for biojs2.0
I can see why you changed it
Sebastian Wilzbach
@wilzbach
Feb 17 2015 02:50
But?
rowlandm
@rowlandm
Feb 17 2015 02:50
But I haven't really got a good overview of everything in the one place
lol
I worked out that I should either have biojs-io-xyz or bio-js-vis-xyz for my packages
Shakeel Shafiq
@thirdknife
Feb 17 2015 02:51
hi @greenify
Sebastian Wilzbach
@wilzbach
Feb 17 2015 02:51
Ah no there is no naming convention
Shakeel Shafiq
@thirdknife
Feb 17 2015 02:52
@greenify can you help me on the drawing lines issue I shared
Sebastian Wilzbach
@wilzbach
Feb 17 2015 02:52
@thirdknife Sry totally forgot to answer
rowlandm
@rowlandm
Feb 17 2015 02:52
oh - ok. I didn't know - I'd probably do that anyway
I think I will try to put together a really basic overview as I'm pretty lost with how things work
That's due to my lack of knowledge about npm and node which I've heard of but never used
Sebastian Wilzbach
@wilzbach
Feb 17 2015 02:55
Oh I am sry
Do you know about the edu
  • edu.biojs.net?
rowlandm
@rowlandm
Feb 17 2015 02:55
Yes - one of the guys mentioned it - it looks good :)
But the first entry in google for biojs is the old website
I realised after about 10 minutes that there must be another new one
Sebastian Wilzbach
@wilzbach
Feb 17 2015 02:56
@thirdknife: I don't get your concrete problem
rowlandm
@rowlandm
Feb 17 2015 02:56
No worries - I think you guys are doing great - just a bit hard for me to get everything at once
Shakeel Shafiq
@thirdknife
Feb 17 2015 02:57
It's more related to d3, I want to add lines with a group of rectangles
Sebastian Wilzbach
@wilzbach
Feb 17 2015 02:57
Yes I wrote to rafa more than ten times to make a redirection, but without luck
rowlandm
@rowlandm
Feb 17 2015 02:58
So where do you fit in then greenify?
from a team perspective?
Sebastian Wilzbach
@wilzbach
Feb 17 2015 02:59
Well we want to update edu anyway, so we will then put more focus on npm & node
Just an open source contributor from Munich :)
rowlandm
@rowlandm
Feb 17 2015 03:00
cool
Basic question - so I don't need to have any standards like in biojs1.0
I just use slush-biojs to build a new package framework
Sebastian Wilzbach
@wilzbach
Feb 17 2015 03:01
Yes I got that but I am on my phone and can't execute your code, so do you get any errors or is the line just not showing up?
@rowlandm slush-biojs is just a helper to bootstrap a new package
And yes at the moment you don't need to extend a biojs core or specify meta information in the js source
Most of the meta information has moved to the package.json
The event system was replaced with biojs-events
rowlandm
@rowlandm
Feb 17 2015 03:04
Oh awesome - thanks for that
Sebastian Wilzbach
@wilzbach
Feb 17 2015 03:04
And to have custom default values one can pick his favorite extend function
However there are some rules about example snippets - basically they should be minimal
rowlandm
@rowlandm
Feb 17 2015 03:06
ok
Sebastian Wilzbach
@wilzbach
Feb 17 2015 03:06
That is why in most cases this custom div is injected
rowlandm
@rowlandm
Feb 17 2015 03:07
yeah right
so the code basically lives in npm online
Sebastian Wilzbach
@wilzbach
Feb 17 2015 03:07
That allows us to reuse the snippet on the registry :(
rowlandm
@rowlandm
Feb 17 2015 03:07
and the biojs registry just points to that?
Sebastian Wilzbach
@wilzbach
Feb 17 2015 03:07
Npm online?
Sorry - I don't have the lingo down yet
Sebastian Wilzbach
@wilzbach
Feb 17 2015 03:08
Well the biojs registry does a lot of magic, but in essence it uses browserify cdn
Browse a visual component and click on edit
Sry I wanted to say :browse any visualization component at the biojs registry
@thirdknife are you still here?
rowlandm
@rowlandm
Feb 17 2015 03:12
yeah - I had a bit of a look
just sent an email about http://www.ebi.ac.uk/Tools/biojs/registry/ to the other guys I know at biojs
see how that goes
Sebastian Wilzbach
@wilzbach
Feb 17 2015 03:13
Wow thanks :)
<script src="https://wzrd.in/bundle/msa@0.3.26"></script>
(this is what I meant with browserify cdn)
rowlandm
@rowlandm
Feb 17 2015 03:17
ok thanks :)
Not sure what that means but I'm sure it will make sense down the road :)
Sebastian Wilzbach
@wilzbach
Feb 17 2015 03:19
Do you have any questions right now?
rowlandm
@rowlandm
Feb 17 2015 03:19
no - I'm good
Sebastian Wilzbach
@wilzbach
Feb 17 2015 03:19
(I changed quite a bit)
rowlandm
@rowlandm
Feb 17 2015 03:19
thanks for your help
Sebastian Wilzbach
@wilzbach
Feb 17 2015 03:20
You are very welcome ;-)
Ah Btw there is a interactive workshop about npm
rowlandm
@rowlandm
Feb 17 2015 03:22
Thanks!
Joey Lin
@linjoey
Feb 17 2015 04:34
@thirdknife if you still need to add lines in the chromosome, try adding the stroke style:
band.append("line")
                                .style('stroke', "black")
                                .attr("x1", 0)
                                .attr("y1", 40)
                                .attr("x2", 20)
                                .attr("y2", 40);
Shakeel Shafiq
@thirdknife
Feb 17 2015 04:35
Okay, checking!
Shakeel Shafiq
@thirdknife
Feb 17 2015 05:20
@linjoey it worked
is it necessary to add storke for line?
Shakeel Shafiq
@thirdknife
Feb 17 2015 05:32
How would I add text?
Abhilash
@abhi3011
Feb 17 2015 08:55
hi i am having problem using sniper, after i do npm run sniper the console shows running localhost9090 but when i open the browser it shows that the webpage is not available am i doing something wrong?
Abhilash
@abhi3011
Feb 17 2015 09:04
also "npm run watch" gives error module-deps not found
Sebastian Wilzbach
@wilzbach
Feb 17 2015 10:34
What os do you use?
It sounds a bit lot something went wrong during your modules installation. Have you noticed anything strange during "npm install"?
Joey Lin
@linjoey
Feb 17 2015 12:14

@thirdknife yes, I believe stroke is necessary for it to show. There're also other svg line attributes you can play around with like stroke-width, though I'd apply them in the CSS file. To append a text element to the band grouping like the lines, you can do so like the lines:

band.append('text')
     .text(function(d){return d.id})
     .attr('y', 24)
     .attr('x', function(d) {return _xscale(d.START.textContent)} );

Again, you'd likely need to apply some css to make it visible, like setting the font size smaller, or rotate it so that they don't overlap, etc.

This message was deleted
Abhilash
@abhi3011
Feb 17 2015 18:12
i use windows
there was problem in installation npm i got it, i use cygwin for unix like commands is it fine?
Sebastian Wilzbach
@wilzbach
Feb 17 2015 18:15

there was problem in installation npm i got it

Oh that was only first guess

i use cygwin for unix like commands is it fine?

yes.

what is the exact error message that you receive when running npm run watch?
can you browse http://localhost:9090/examples?
Abhilash
@abhi3011
Feb 17 2015 18:24
it module-deps not found
Sebastian Wilzbach
@wilzbach
Feb 17 2015 18:24
don't you get a stack trace?
Abhilash
@abhi3011
Feb 17 2015 18:31
nope ,i think due to slow internet all the dependencies are not installed properly will install again
Prasun Anand
@prasunanand
Feb 17 2015 19:01
Getting this error in slush biojs after i reinstalled slush-biojs
http://pastebin.com/YV0hjM8K
Sebastian Wilzbach
@wilzbach
Feb 17 2015 19:03
@prasunanand: what options did you select?
sry - you posted that too :)
Prasun Anand
@prasunanand
Feb 17 2015 19:03
:)
tyreek
@tyreek
Feb 17 2015 19:05
(biojs-registry via irc) BioJS package update: slush-biojs to 0.7.10 by @BioJS
Sebastian Wilzbach
@wilzbach
Feb 17 2015 19:06
should be fixed in 7142e20d0e3b61ee80c03b5d4f2f7197acc08f91 - version 0.7.10 :)
thanks for letting us know!
Prasun Anand
@prasunanand
Feb 17 2015 19:06
Thanks !
:)
tyreek
@tyreek
Feb 17 2015 23:35
(JohnhyCashIRC via irc) hello
(jessfeeney via irc) JohnhyCashIRC: don't ask to ask - just ask. whats up?
(JohnhyCashIRC via irc) not a whole lot what about you
(JohnhyCashIRC via irc) glad to get a reponse most of these channels are idle
(JohnhyCashIRC via irc) ok so im not ure you can help me out here but i need some specified topic channels
(jessfeeney via irc) JohnhyCashIRC: I think you are in the wrong channel?
(JohnhyCashIRC via irc) id say but im new to irc and need help
(JohnhyCashIRC via irc) like dumbed down alot
tyreek
@tyreek
Feb 17 2015 23:41
(jessfeeney via irc) ask the people at #freenode they will be able to help or redirect you ;-)
(JohnhyCashIRC via irc) thanks i appreciate it